Publications by authors named "Aparna Prasad"

35 Publications

The Temple Grandin Genome: Comprehensive Analysis in a Scientist with High-Functioning Autism.

J Pers Med 2020 Dec 29;11(1). Epub 2020 Dec 29.

The Center for Neurological and Neurodevelopmental Health, Voorhees, NJ 08043, USA.

Autism spectrum disorder (ASD) is a heterogeneous condition with a complex genetic etiology. The objective of this study is to identify the complex genetic factors that underlie the ASD phenotype and other clinical features of Professor Temple Grandin, an animal scientist and woman with high-functioning ASD. Identifying the underlying genetic cause for ASD can impact medical management, personalize services and treatment, and uncover other medical risks that are associated with the genetic diagnosis. Prof. Grandin underwent chromosomal microarray analysis, whole exome sequencing, and whole genome sequencing, as well as a comprehensive clinical and family history intake. The raw data were analyzed in order to identify possible genotype-phenotype correlations. Genetic testing identified variants in three genes (, , and ) that are candidate risk factors for ASD. We identified variants in and , reported to be disease-associated in previous studies, which are likely to contribute to some of her additional clinical features. Moreover, candidate variants in genes encoding metabolic enzymes and transporters were identified, some of which suggest potential therapies. This case report describes the genomic findings in Prof. Grandin and it serves as an example to discuss state-of-the-art clinical diagnostics for individuals with ASD, as well as the medical, logistical, and economic hurdles that are involved in clinical genetic testing for an individual on the autism spectrum.
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http://dx.doi.org/10.3390/jpm11010021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824360PMC
December 2020

Dually localised proteins found in both the apicoplast and mitochondrion utilize the Golgi-dependent pathway for apicoplast targeting in Toxoplasma gondii.

Biol Cell 2021 Jan 23;113(1):58-78. Epub 2020 Nov 23.

Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.

Background Information: Like other apicomplexan parasites, Toxoplasma gondii harbours a four-membraned endosymbiotic organelle - the apicoplast. Apicoplast proteins are nuclear encoded and trafficked to the organelle through the endoplasmic reticulum (ER). From the ER to the apicoplast, two distinct protein trafficking pathways can be used. One such pathway is the cell's secretory pathway involving the Golgi, whereas the other is a unique Golgi-independent pathway. Using different experimental approaches, many apicoplast proteins have been shown to utilize the Golgi-independent pathway, whereas a handful of reports show that a few proteins use the Golgi-dependent pathway. This has led to an emphasis towards the unique Golgi-independent pathway when apicoplast protein trafficking is discussed in the literature. Additionally, the molecular features that drive proteins to each pathway are not known.

Results: In this report, we systematically test eight apicoplast proteins, using a C-terminal HDEL sequence to assess the role of the Golgi in their transport. We demonstrate that dually localised proteins of the apicoplast and mitochondrion (TgSOD2, TgTPx1/2 and TgACN/IRP) are trafficked through the Golgi, whereas proteins localised exclusively to the apicoplast are trafficked independent of the Golgi. Mutants of the dually localised proteins that localised exclusively to the apicoplast also showed trafficking through the Golgi. Phylogenetic analysis of TgSOD2, TgTPx1/2 and TgACN/IRP suggested that the evolutionary origins of TgSOD2 and TgTPx1/2 lie in the mitochondrion, whereas TgACN/IRP appears to have originated from the apicoplast.

Conclusions And Significance: Collectively, with these results, for the first time, we establish that the driver of the Golgi-dependent trafficking route to the apicoplast is the dual localisation of the protein to the apicoplast and the mitochondrion.
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http://dx.doi.org/10.1111/boc.202000050DOI Listing
January 2021

Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons.

BMC Genomics 2020 Aug 5;21(1):540. Epub 2020 Aug 5.

Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.

Background: The South African claw-toed frog, Xenopus laevis, is uniquely suited for studying differences between regenerative and non-regenerative responses to CNS injury within the same organism, because some CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs. Tissues from these CNS regions (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) were used in a three-way RNA-seq study of axotomized CNS axons to identify potential core gene expression programs for successful CNS axon regeneration.

Results: Despite tissue-specific changes in expression dominating the injury responses of each tissue, injury-induced changes in gene expression were nonetheless shared between the two axon-regenerative CNS regions that were not shared with the non-regenerative region. These included similar temporal patterns of gene expression and over 300 injury-responsive genes. Many of these genes and their associated cellular functions had previously been associated with injury responses of multiple tissues, both neural and non-neural, from different species, thereby demonstrating deep phylogenetically conserved commonalities between successful CNS axon regeneration and tissue regeneration in general. Further analyses implicated the KEGG adipocytokine signaling pathway, which links leptin with metabolic and gene regulatory pathways, and a novel gene regulatory network with genes regulating chromatin accessibility at its core, as important hubs in the larger network of injury response genes involved in successful CNS axon regeneration.

Conclusions: This study identifies deep, phylogenetically conserved commonalities between CNS axon regeneration and other examples of successful tissue regeneration and provides new targets for studying the molecular underpinnings of successful CNS axon regeneration, as well as a guide for distinguishing pro-regenerative injury-induced changes in gene expression from detrimental ones in mammals.
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http://dx.doi.org/10.1186/s12864-020-06954-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7430912PMC
August 2020

Critical exon indexing improves clinical interpretation of copy number variants in neurodevelopmental disorders.

Neurol Genet 2019 Dec 6;5(6):e378. Epub 2019 Dec 6.

Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada.

Objective: To evaluate a new tool to aid interpretation of copy number variants (CNVs) in individuals with neurodevelopmental disabilities.

Methods: Critical exon indexing (CEI) was used to identify genes with critical exons (CEGs) from clinically reported CNVs, which may contribute to neurodevelopmental disorders (NDDs). The 742 pathogenic CNVs and 1,363 variants of unknown significance (VUS) identified by chromosomal microarray analysis in 5,487 individuals with NDDs were subjected to CEI to identify CEGs. CEGs identified in a subsequent random series of VUS were evaluated for relevance to CNV interpretation.

Results: CEI identified a total of 2,492 unique CEGs in pathogenic CNVs and 953 in VUS compared with 259 CEGs in 6,965 CNVs from 873 controls. These differences are highly significant ( < 0.00001) whether compared as frequency, average, or normalized by CNV size. Twenty-one percent of VUS CEGs were not represented in Online Mendelian Inheritance in Man, highlighting limitations of existing resources for identifying potentially impactful genes within CNVs. CEGs were highly correlated with other indices and known pathways of relevance. Separately, 136 random VUS reports were reevaluated, and 76% of CEGs had not been commented on. In multiple cases, further investigation yielded additional relevant literature aiding interpretation. As one specific example, we discuss as a CEG, which likely alters interpretation of several reported duplication VUS in the Williams-Beuren region.

Conclusions: Application of CEI to CNVs in individuals with NDDs can identify genes of potential clinical relevance, aid laboratories in effectively searching the clinical literature, and support the clinical reporting of poorly annotated VUS.
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http://dx.doi.org/10.1212/NXG.0000000000000378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927359PMC
December 2019

Rare copy number variations affecting the synaptic gene DMXL2 in neurodevelopmental disorders.

J Neurodev Disord 2019 02 7;11(1). Epub 2019 Feb 7.

The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.

Background: Ultra-rare genetic variants, including non-recurrent copy number variations (CNVs) affecting important dosage-sensitive genes, are important contributors to the etiology of neurodevelopmental disorders (NDDs). Pairing family-based whole-genome sequencing (WGS) with detailed phenotype data can enable novel gene associations in NDDs.

Methods: We performed WGS of six members from a three-generation family, where three individuals each had a spectrum of features suggestive of a NDD. CNVs and sequence-level variants were identified and further investigated in disease and control databases.

Results: We identified a novel 252-kb deletion at 15q21 that overlaps the synaptic gene DMXL2 and the gene GLDN. The microdeletion segregated in NDD-affected individuals. Additional rare inherited and de novo sequence-level variants were found that may also be involved, including a missense change in GRIK5. Multiple CNVs and loss-of-function sequence variants affecting DMXL2 were discovered in additional unrelated individuals with a range of NDDs.

Conclusions: Disruption of DMXL2 may predispose to NDDs including autism spectrum disorder. The robust interpretation of private variants requires a multifaceted approach that incorporates multigenerational pedigrees and genome-wide and population-scale data.
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http://dx.doi.org/10.1186/s11689-019-9263-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366120PMC
February 2019

Interpretation errors in focused cardiac ultrasound by novice pediatric emergency medicine fellow sonologists.

Crit Ultrasound J 2018 Dec 9;10(1):33. Epub 2018 Dec 9.

Department of Emergency Medicine and Trauma Services, Children's National Medical Center, Washington, DC, USA.

Background: Focused cardiac ultrasound (FOCUS) is a core competency for pediatric emergency medicine (PEM) fellows. The objectives of this study were (1) to evaluate test characteristics of PEM-fellow-performed FOCUS for pericardial effusion and diminished cardiac function and (2) to assess image interpretation independent of image acquisition.

Methods: PEM fellows performed and interpreted FOCUS on patients who also received cardiology service echocardiograms, the reference standard. Subsequently, eight different PEM fellows remotely interpreted a subset of the PEM-acquired and cardiology-acquired echocardiograms.

Results: Eight PEM fellows performed 54 FOCUS exams, of which two had pericardial effusion and four had diminished function. PEM fellow FOCUS had a sensitivity of 50.0% (95% CI 9.19-90.8) and specificity of 100.0% (95% CI 91.1-100.0) for detecting diminished function, and sensitivity of 50.0% (95% CI 2.67-97.33) and specificity of 98.1% (95% CI 88.42-99.9) for detecting pericardial effusions. When PEM fellows remotely interpreted 15 echocardiograms, the sensitivity was 81.3% (95% CI 70.7-88.8) and specificity 75% (95% CI 67.0-81.0) for detecting diminished function, and sensitivity of 76.3% (95% CI 65.0-85.0) and specificity 94.4% (95% CI 89.0-97.0) for detecting pericardial effusion. There were no differences in sensitivity and specificity of PEM fellows' interpretation of FOCUS studies compared to their interpretation of cardiology echocardiograms. Interrater reliability for interpretation of remote images (kappa) was 0.66 (95% CI 0.59-0.73) for effusion and 0.31 (95% CI 0.24-0.38) for function among the fellows.

Conclusion: Novice PEM fellow sonologists (a physician who performs and interprets ultrasound) in the majority of instances were able to acquire and remotely interpret FOCUS images with limited training. However, they made real-time interpretation errors and likely need further training to incorporate real-time image acquisition and interpretation into their practice.
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http://dx.doi.org/10.1186/s13089-018-0113-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286908PMC
December 2018

The transcription factor Tfap2e/AP-2ε plays a pivotal role in maintaining the identity of basal vomeronasal sensory neurons.

Dev Biol 2018 09 19;441(1):67-82. Epub 2018 Jun 19.

Department of Biological Sciences, University at Albany, Albany, NY 12222, USA. Electronic address:

The identity of individual neuronal cell types is defined and maintained by the expression of specific combinations of transcriptional regulators that control cell type-specific genetic programs. The epithelium of the vomeronasal organ of mice contains two major types of vomeronasal sensory neurons (VSNs): 1) the apical VSNs which express vomeronasal 1 receptors (V1r) and the G-protein subunit Gαi2 and; 2) the basal VSNs which express vomeronasal 2 receptors (V2r) and the G-protein subunit Gαo. Both cell types originate from a common pool of progenitors and eventually acquire apical or basal identity through largely unknown mechanisms. The transcription factor AP-2ε, encoded by the Tfap2e gene, plays a role in controlling the development of GABAergic interneurons in the main and accessory olfactory bulb (AOB), moreover AP-2ε has been previously described to be expressed in the basal VSNs. Here we show that AP-2ε is expressed in post-mitotic VSNs after they commit to the basal differentiation program. Loss of AP-2ε function resulted in reduced number of basal VSNs and in an increased number of neurons expressing markers of the apical lineage. Our work suggests that AP-2ε, which is expressed in late phases of differentiation, is not needed to initiate the apical-basal differentiation dichotomy but for maintaining the basal VSNs' identity. In AP-2ε mutants we observed a large number of cells that entered the basal program can express apical genes, our data suggest that differentiated VSNs of mice retain a notable level of plasticity.
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http://dx.doi.org/10.1016/j.ydbio.2018.06.007DOI Listing
September 2018

Clinical significance of copy number variants involving KANK1 in patients with neurodevelopmental disorders.

Eur J Med Genet 2019 Jan 3;62(1):15-20. Epub 2018 May 3.

Lineagen, Inc., Salt Lake City, UT, United States. Electronic address:

Copy number variants (CNV)s involving KANK1 are generally classified as variants of unknown significance. Several clinical case reports suggest that the loss of KANK1 on chromosome 9p24.3 has potential impact on neurodevelopment. These case studies are inconsistent in terms of patient phenotype and suspected pattern of inheritance. Further complexities arise because these published reports utilize a variety of genetic testing platforms with varying resolution of the 9p region; this ultimately causes uncertainty about the impacted genomic coordinates and gene transcripts. Beyond these case reports, large case-control studies and publicly available databases statistically cast doubt as to whether variants of KANK1 are clinically significant. However, these large data sources are neither easily extracted nor uniformly applied to clinical interpretation. In this report we provide an updated analysis of the data on this locus and its potential clinical relevance. This is based on a review of the literature as well as 28 patients who harbor a single copy number variant involving KANK1 with or without DOCK8 (27 of whom are not published previously) identified by our clinical laboratory using an ultra-high resolution chromosomal microarray analysis. We note that 13 of 16 patients have a documented diagnosis of autism spectrum disorder (ASD) while only two, with documented perinatal complications, have a documented diagnosis of cerebral palsy (CP). A careful review of the CNVs suggests a transcript-specific effect. After evaluation of our case series and reconsideration of the literature, we propose that KANK1 aberrations do not frequently cause CP but cannot exclude that they represent a risk factor for ASD, especially when the coding region of the shorter, alternate KANK1 transcript (termed "transcript 4" in the UCSC Genome Browser) is impacted.
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http://dx.doi.org/10.1016/j.ejmg.2018.04.012DOI Listing
January 2019

Clinical utility of exome sequencing in individuals with large homozygous regions detected by chromosomal microarray analysis.

BMC Med Genet 2018 03 20;19(1):46. Epub 2018 Mar 20.

Lineagen, Inc., 2677 East Parleys Way, Salt Lake City, UT, 84109, USA.

Background: Chromosomal microarray analysis (CMA) is recommended as the first-tier clinical diagnostic test for individuals with developmental disabilities. In addition to detecting copy number variations, CMA platforms with single nucleotide polymorphism probes can detect large homozygous regions within the genome, which represent potential risk for recessively inherited disorders.

Methods: To determine the frequency in which pathogenic or likely pathogenic variants can be detected in these regions of homozygosity, we performed whole exome sequencing (WES) in 53 individuals where homozygosity was detected by CMA. These patients were referred to our clinical laboratory for a variety of neurodevelopmental conditions including autism spectrum disorder, developmental delay, epilepsy, intellectual disability and microcephaly.

Results: In 11.3% (6/53) of cases, the analysis of homozygous variants revealed pathogenic or likely pathogenic variants in GJB2, TPP1, SLC25A15, TYR, PCCB, and NDUFV2 which are implicated in a variety of diseases. The evaluation of heterozygous variants with autosomal dominant inheritance, compound heterozygotes and variants with X-linked inheritance revealed pathogenic or likely pathogenic variants in PNPLA4, CADM1, HBB, SOS1, SFTPC, OTC and ASMT in 15.1% (8/53) of cases. Two of these patients harbored both homozygous and heterozygous variants relevant to their phenotypes (TPP1 and OTC; GJB2 and ASMT).

Conclusions: Our study highlights the clinical utility of WES in individuals whose CMA uncovers homozygosity. Importantly, we show that when the phenotype is complex and homozygosity levels are high, WES can identify a significant number of relevant variants that explain neurodevelopmental phenotypes, and these mutations may lie outside of the regions of homozygosity, suggesting that the appropriate follow up test is WES rather than targeted sequencing.
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http://dx.doi.org/10.1186/s12881-018-0555-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859484PMC
March 2018

1q21.1 Duplication syndrome and epilepsy: Case report and review.

Neurol Genet 2018 Feb 18;4(1):e219. Epub 2018 Jan 18.

Department of Pediatrics (I.G.), New York Presbyterian Brooklyn Methodist Hospital, Brooklyn; Center for Neurological and Neurodevelopmental Health (R.S.), Voorhees Township, NJ; and Lineagen (A.P.), Salt Lake City, UT.

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http://dx.doi.org/10.1212/NXG.0000000000000219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773857PMC
February 2018

The terminal nerve plays a prominent role in GnRH-1 neuronal migration independent from proper olfactory and vomeronasal connections to the olfactory bulbs.

Biol Open 2017 Oct 15;6(10):1552-1568. Epub 2017 Oct 15.

Department of Biological Sciences, University at Albany, Albany, NY 12222, USA

Gonadotropin-releasing hormone-1 (GnRH-1) neurons (GnRH-1 ns) migrate from the developing olfactory pit into the hypothalamus during embryonic development. Migration of the GnRH-1 neurons is required for mammalian reproduction as these cells control release of gonadotropins from the anterior pituitary gland. Disturbances in GnRH-1 ns migration, GnRH-1 synthesis, secretion or signaling lead to varying degrees of hypogonadotropic hypogonadism (HH), which impairs pubertal onset and fertility. HH associated with congenital olfactory defects is clinically defined as Kallmann Syndrome (KS). The association of olfactory defects with HH in KS suggested a potential direct relationship between defective olfactory axonal routing, lack of olfactory bulbs (OBs) and aberrant GnRH-1 ns migration. However, it has never been experimentally proven that the formation of axonal connections of the olfactory/vomeronasal neurons to their functional targets are necessary for the migration of GnRH-1 ns to the hypothalamus. Loss-of-function of the homeobox gene leads to the lack of proper formation of the OBs with abnormal axonal termination of olfactory sensory neurons ( Yoshihara et al., 2005). Our data prove that correct development of the OBs and axonal connection of the olfactory/vomeronasal sensory neurons to the forebrain are not required for GnRH-1 ns migration, and suggest that the terminal nerve, which forms the GnRH-1 migratory scaffold, follows different guidance cues and differs in gene expression from olfactory/vomeronasal sensory neurons.
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http://dx.doi.org/10.1242/bio.029074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5665474PMC
October 2017

Markers of Cardiovascular Dysfunction in Adolescents With Anorexia Nervosa.

Glob Pediatr Health 2017 29;4:2333794X17727423. Epub 2017 Aug 29.

Goryeb Children's Hospital, Atlantic Health System, Morristown, NJ, USA.

. Cardiovascular complications contribute to the high morbidity and mortality rate among children with anorexia nervosa (AN). Advances in cardiac imaging permit a more comprehensive assessment of myocardial performance in children that could not be previously obtained with conventional imaging. Myocardial strain analysis is an emerging quantitative echocardiographic technique to characterize global and regional ventricular function in children. . To assess global and regional left ventricular (LV0 function in children newly diagnosed with AN with conventional and quantitative 2-dimensional speckle tracking echocardiographic (2DSTE)-derived strain imaging. . In a cross-sectional study of 30 patients with AN () and 14 age-, sex-, and race-matched healthy children, markers of cardiovascular risk, conventional and 2DSTE measures of LV function, and structure were evaluated and compared. The AN cohort was further stratified by behavioral patterns (restrict, exercise, or purge). . Conventional measures and LV global strain were similar between controls and children with AN. A subgroup of AN children with purging behavior had LV remodeling characterized by significantly decreased LV mass index. Regional ventricular function at the apex, as measured by strain, was also decreased in all AN patients. Percent change from ideal body weight, body mass index -score, electrolyte profiles, heart rate, and blood pressure were similar. . Subclinical regional ventricular dysfunction is present in children with AN. Ventricular remodeling exists in a subgroup of children with AN in association with purging behavior. Future studies may utilize strain imaging to identify those AN patients who are at an increased risk for developing significant cardiac dysfunction.
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http://dx.doi.org/10.1177/2333794X17727423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580842PMC
August 2017

Chromosomal Microarray Analysis of Consecutive Individuals with Autism Spectrum Disorders Using an Ultra-High Resolution Chromosomal Microarray Optimized for Neurodevelopmental Disorders.

Int J Mol Sci 2016 Dec 9;17(12). Epub 2016 Dec 9.

Departments of Psychiatry, Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, UT 66160, USA.

Copy number variants (CNVs) detected by chromosomal microarray analysis (CMA) significantly contribute to understanding the etiology of autism spectrum disorder (ASD) and other related conditions. In recognition of the value of CMA testing and its impact on medical management, CMA is in medical guidelines as a first-tier test in the evaluation of children with these disorders. As CMA becomes adopted into routine care for these patients, it becomes increasingly important to report these clinical findings. This study summarizes the results of over 4 years of CMA testing by a CLIA-certified clinical testing laboratory. Using a 2.8 million probe microarray optimized for the detection of CNVs associated with neurodevelopmental disorders, we report an overall CNV detection rate of 28.1% in 10,351 consecutive patients, which rises to nearly 33% in cases without ASD, with only developmental delay/intellectual disability (DD/ID) and/or multiple congenital anomalies (MCA). The overall detection rate for individuals with ASD is also significant at 24.4%. The detection rate and pathogenic yield of CMA vary significantly with the indications for testing, age, and gender, as well as the specialty of the ordering doctor. We note discrete differences in the most common recurrent CNVs found in individuals with or without a diagnosis of ASD.
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http://dx.doi.org/10.3390/ijms17122070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5187870PMC
December 2016

Identification of Gene Mutations and Fusion Genes in Patients with Sézary Syndrome.

J Invest Dermatol 2016 07 30;136(7):1490-1499. Epub 2016 Mar 30.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain; Experimental Genetics, Sidra Medical and Research Centre, Doha, Qatar. Electronic address:

Sézary syndrome is a leukemic form of cutaneous T-cell lymphoma with an aggressive clinical course. The genetic etiology of the disease is poorly understood, with chromosomal abnormalities and mutations in some genes being involved in the disease. The goal of our study was to understand the genetic basis of the disease by looking for driver gene mutations and fusion genes in 15 erythrodermic patients with circulating Sézary cells, 14 of them fulfilling the diagnostic criteria of Sézary syndrome. We have discovered genes that could be involved in the pathogenesis of Sézary syndrome. Some of the genes that are affected by somatic point mutations include ITPR1, ITPR2, DSC1, RIPK2, IL6, and RAG2, with some of them mutated in more than one patient. We observed several somatic copy number variations shared between patients, including deletions and duplications of large segments of chromosome 17. Genes with potential function in the T-cell receptor signaling pathway and tumorigenesis were disrupted in Sézary syndrome patients, for example, CBLB, RASA2, BCL7C, RAMP3, TBRG4, and DAD1. Furthermore, we discovered several fusion events of interest involving RASA2, NFKB2, BCR, FASN, ZEB1, TYK2, and SGMS1. Our work has implications for the development of potential therapeutic approaches for this aggressive disease.
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http://dx.doi.org/10.1016/j.jid.2016.03.024DOI Listing
July 2016

Utility of hand-held echocardiography in outpatient pediatric cardiology management.

Pediatr Cardiol 2014 Dec 10;35(8):1379-86. Epub 2014 Jun 10.

Division of Cardiology, Children's National Medical Center, Washington, DC, USA,

Adult patient series have shown hand-held echocardiography (echo) units (HHE) to be accurate for rapid diagnosis and triage. This is the first study to evaluate the ability of HHE to inform decision making in outpatient pediatric cardiology. New pediatric cardiology patients in outpatient clinics staffed by six pediatric cardiologists (experience 1-17 years) were prospectively enrolled if an echocardiogram (echo) was ordered during their initial visit. After history and physical examination and before a standard echo, the cardiologists performed a bedside HHE examination (GE Vscan 1.7-3.8 MHz), documented findings, and made a clinical decision. Diagnoses and decisions based on HHE were compared with final management after the standard echo. The study enrolled 101 subjects (ages 9 days to 19 years). The cardiologists considered HHE imaging adequate for decision making for 80 of the 101 subjects. For 77 of the 80 subjects with acceptable HHE imaging (68/68 normal and 9/12 abnormal standard echoes), the HHE-based primary diagnoses and decisions agreed with the final management. The sensitivity of HHE was 75 % (95 % confidence interval [CI] 43-94 %) and the positive predictive value 100 % (95 % CI 66-100 %) for pediatric heart disease. The agreement between standard echocardiography and HHE imaging was substantial (κ = 0.82). Excluding one of the least experienced cardiologists, HHE provided the basis for correct cardiac diagnoses and management for all the subjects with acceptable HHE imaging (58/58 normal and 9/9 abnormal echoes). In outpatient pediatric cardiology, HHE has potential as a tool to complement physical examination. Further investigation is needed to evaluate how value improves with clinical experience.
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http://dx.doi.org/10.1007/s00246-014-0940-4DOI Listing
December 2014

Rare exonic deletions implicate the synaptic organizer Gephyrin (GPHN) in risk for autism, schizophrenia and seizures.

Hum Mol Genet 2013 May 7;22(10):2055-66. Epub 2013 Feb 7.

The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children,Toronto, ON, Canada.

The GPHN gene codes for gephyrin, a key scaffolding protein in the neuronal postsynaptic membrane, responsible for the clustering and localization of glycine and GABA receptors at inhibitory synapses. Gephyrin has well-established functional links with several synaptic proteins that have been implicated in genetic risk for neurodevelopmental disorders such as autism spectrum disorder (ASD), schizophrenia and epilepsy including the neuroligins (NLGN2, NLGN4), the neurexins (NRXN1, NRXN2, NRXN3) and collybistin (ARHGEF9). Moreover, temporal lobe epilepsy has been linked to abnormally spliced GPHN mRNA lacking exons encoding the G-domain of the gephyrin protein, potentially arising due to cellular stress associated with epileptogenesis such as temperature and alkalosis. Here, we present clinical and genomic characterization of six unrelated subjects, with a range of neurodevelopmental diagnoses including ASD, schizophrenia or seizures, who possess rare de novo or inherited hemizygous microdeletions overlapping exons of GPHN at chromosome 14q23.3. The region of common overlap across the deletions encompasses exons 3-5, corresponding to the G-domain of the gephyrin protein. These findings, together with previous reports of homozygous GPHN mutations in connection with autosomal recessive molybdenum cofactor deficiency, will aid in clinical genetic interpretation of the GPHN mutation spectrum. Our data also add to the accumulating evidence implicating neuronal synaptic gene products as key molecular factors underlying the etiologies of a diverse range of neurodevelopmental conditions.
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http://dx.doi.org/10.1093/hmg/ddt056DOI Listing
May 2013

A discovery resource of rare copy number variations in individuals with autism spectrum disorder.

G3 (Bethesda) 2012 Dec 1;2(12):1665-85. Epub 2012 Dec 1.

The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto M5G 1L7, Canada.

The identification of rare inherited and de novo copy number variations (CNVs) in human subjects has proven a productive approach to highlight risk genes for autism spectrum disorder (ASD). A variety of microarrays are available to detect CNVs, including single-nucleotide polymorphism (SNP) arrays and comparative genomic hybridization (CGH) arrays. Here, we examine a cohort of 696 unrelated ASD cases using a high-resolution one-million feature CGH microarray, the majority of which were previously genotyped with SNP arrays. Our objective was to discover new CNVs in ASD cases that were not detected by SNP microarray analysis and to delineate novel ASD risk loci via combined analysis of CGH and SNP array data sets on the ASD cohort and CGH data on an additional 1000 control samples. Of the 615 ASD cases analyzed on both SNP and CGH arrays, we found that 13,572 of 21,346 (64%) of the CNVs were exclusively detected by the CGH array. Several of the CGH-specific CNVs are rare in population frequency and impact previously reported ASD genes (e.g., NRXN1, GRM8, DPYD), as well as novel ASD candidate genes (e.g., CIB2, DAPP1, SAE1), and all were inherited except for a de novo CNV in the GPHN gene. A functional enrichment test of gene-sets in ASD cases over controls revealed nucleotide metabolism as a potential novel pathway involved in ASD, which includes several candidate genes for follow-up (e.g., DPYD, UPB1, UPP1, TYMP). Finally, this extensively phenotyped and genotyped ASD clinical cohort serves as an invaluable resource for the next step of genome sequencing for complete genetic variation detection.
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http://dx.doi.org/10.1534/g3.112.004689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516488PMC
December 2012

Anergy in CD4 memory T lymphocytes. II. Abrogation of TCR-induced formation of membrane signaling complexes.

Cell Immunol 2012 Mar-Apr;276(1-2):26-34. Epub 2012 May 19.

The Department of Biomedical Sciences, The School of Public Health, The University at Albany, Albany, New York 12201-0509, United States.

Memory and naive CD4 T cells have unique regulatory pathways for self/non-self discrimination. A memory cell specific regulatory pathway was revealed using superantigens to trigger the TCR. Upon stimulation by bacterial superantigens, like staphylococcal enterotoxin B (SEB), TCR proximal signaling is impaired leading to clonal tolerance (anergy). In the present report, we show that memory cell anergy results from the sequestration of the protein tyrosine kinase ZAP-70 away from the TCR/CD3ζ chain. During SEB-induced signaling, ZAP-70 is excluded from both detergent-resistant membrane microdomains and the immunological synapse, thus blocking downstream signaling. We also show that the mechanism underlying memory cell anergy must involve Fyn kinase, given that the suppression of Fyn activity restores the movement of ZAP-70 to the immunological synapse, TCR proximal signaling, and cell proliferation. Thus, toleragens, including microbial toxins, may modulate memory responses by targeting the organizational structure of memory cell signaling complexes.
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http://dx.doi.org/10.1016/j.cellimm.2012.05.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399040PMC
October 2012

SHANK1 Deletions in Males with Autism Spectrum Disorder.

Am J Hum Genet 2012 May 12;90(5):879-87. Epub 2012 Apr 12.

The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.

Recent studies have highlighted the involvement of rare (<1% frequency) copy-number variations and point mutations in the genetic etiology of autism spectrum disorder (ASD); these variants particularly affect genes involved in the neuronal synaptic complex. The SHANK gene family consists of three members (SHANK1, SHANK2, and SHANK3), which encode scaffolding proteins required for the proper formation and function of neuronal synapses. Although SHANK2 and SHANK3 mutations have been implicated in ASD and intellectual disability, the involvement of SHANK1 is unknown. Here, we assess microarray data from 1,158 Canadian and 456 European individuals with ASD to discover microdeletions at the SHANK1 locus on chromosome 19. We identify a hemizygous SHANK1 deletion that segregates in a four-generation family in which male carriers--but not female carriers--have ASD with higher functioning. A de novo SHANK1 deletion was also detected in an unrelated male individual with ASD with higher functioning, and no equivalent SHANK1 mutations were found in >15,000 controls (p = 0.009). The discovery of apparent reduced penetrance of ASD in females bearing inherited autosomal SHANK1 deletions provides a possible contributory model for the male gender bias in autism. The data are also informative for clinical-genetics interpretations of both inherited and sporadic forms of ASD involving SHANK1.
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http://dx.doi.org/10.1016/j.ajhg.2012.03.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376495PMC
May 2012

Rare deletions at the neurexin 3 locus in autism spectrum disorder.

Am J Hum Genet 2012 Jan 29;90(1):133-41. Epub 2011 Dec 29.

Program in Genetics and Genome Biology, The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada.

The three members of the human neurexin gene family, neurexin 1 (NRXN1), neurexin 2 (NRXN2), and neurexin 3 (NRXN3), encode neuronal adhesion proteins that have important roles in synapse development and function. In autism spectrum disorder (ASD), as well as in other neurodevelopmental conditions, rare exonic copy-number variants and/or point mutations have been identified in the NRXN1 and NRXN2 loci. We present clinical characterization of four index cases who have been diagnosed with ASD and who possess rare inherited or de novo microdeletions at 14q24.3-31.1, a region that overlaps exons of the alpha and/or beta isoforms of NRXN3. NRXN3 deletions were found in one father with subclinical autism and in a carrier mother and father without formal ASD diagnoses, indicating issues of penetrance and expressivity at this locus. Notwithstanding these clinical complexities, this report on ASD-affected individuals who harbor NRXN3 exonic deletions advances the understanding of the genetic etiology of autism, further enabling molecular diagnoses.
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http://dx.doi.org/10.1016/j.ajhg.2011.11.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3257896PMC
January 2012

The First Type III Domain of Fibronectin is Associated with the Expression of Cytokines within the Lung Tumor Microenvironment.

J Cancer 2011 27;2:478-83. Epub 2011 Sep 27.

1. Center for Cell Biology and Cancer Research, Albany Medical College, Albany, New York, USA.

Recent studies have pointed to changes in tissue mechanics as a contributory element to the development of malignancies. Increased tissue rigidity is associated with the unfolding of the Type III domains of fibronectin within the extracellular matrix. The consequences of this unfolding on cellular functions within the lung are not well understood. In the present study, we evaluated the effect of a peptide representing a partially unfolded intermediate of the first Type III repeat of fibronectin (FnIII-1c) on inflammatory gene expression in adult human lung fibroblast cells. FnIII-1c induced expression of cytokines, CXCL1-3, IL-8 and TNF-α, by lung fibroblast cells. The increase in IL-8 expression was dependent on Toll-like receptor 2 and NFκB. Immunohistochemistry of tissue arrays representing squamous cell carcinoma of the lung revealed extensive stromal staining for IL-8 and fibronectin fibrils which were co-aligned with myofibroblasts. These data suggest a model in which unfolding of FnIII domains secondary to myofibroblast-generated tension may induce the release of cytokines by stromal fibroblasts present within the lung tumor.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187932PMC
http://dx.doi.org/10.7150/jca.2.478DOI Listing
November 2011

Mechanisms of cell death of thymocytes induced by polyunsaturated, monounsaturated and trans-fatty acids.

J Cell Biochem 2011 Dec;112(12):3863-71

Institute for Health and the Environment, University at Albany, Rensselaer, NY 12144, USA.

Polyunsaturated fatty acids (PUFAs) are rapidly cytotoxic to isolated murine thymocytes, and the degree of cell death has been correlated with changes in membrane fluidity, elevation of intracellular calcium concentration and generation of reactive oxygen species. We have compared the degree of cell death and increase in membrane fluidity of C-20 and C-22 omega-3 and 6 PUFAs to those induced by monounsaturated and trans-fatty acids, and find that concentrations which induce comparable increases in membrane fluidity do not cause comparable cell death. The C-18 omega-6 causes a decrease in membrane fluidity, yet is the most potent in causing cell death. Omega-6 PUFAs are more cytotoxic than omega-3 PUFAs, while monounsaturated and trans-fats show little cytotoxicity and only at much higher concentrations. Cell death is preceded by reductions of both plasma and mitochondrial membrane potential, and occurs via apoptosis. These results indicate that cell death is due to mechanisms other than changes in membrane fluidity.
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http://dx.doi.org/10.1002/jcb.23319DOI Listing
December 2011

Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants.

Nat Biotechnol 2011 May 8;29(6):512-20. Epub 2011 May 8.

The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.

We have systematically compared copy number variant (CNV) detection on eleven microarrays to evaluate data quality and CNV calling, reproducibility, concordance across array platforms and laboratory sites, breakpoint accuracy and analysis tool variability. Different analytic tools applied to the same raw data typically yield CNV calls with <50% concordance. Moreover, reproducibility in replicate experiments is <70% for most platforms. Nevertheless, these findings should not preclude detection of large CNVs for clinical diagnostic purposes because large CNVs with poor reproducibility are found primarily in complex genomic regions and would typically be removed by standard clinical data curation. The striking differences between CNV calls from different platforms and analytic tools highlight the importance of careful assessment of experimental design in discovery and association studies and of strict data curation and filtering in diagnostics. The CNV resource presented here allows independent data evaluation and provides a means to benchmark new algorithms.
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http://dx.doi.org/10.1038/nbt.1852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270583PMC
May 2011

A genome-wide scan for common alleles affecting risk for autism.

Hum Mol Genet 2010 Oct 27;19(20):4072-82. Epub 2010 Jul 27.

Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland.

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
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http://dx.doi.org/10.1093/hmg/ddq307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947401PMC
October 2010

Role of calcium and ROS in cell death induced by polyunsaturated fatty acids in murine thymocytes.

J Cell Physiol 2010 Nov;225(3):829-36

Department of Environmental Health Sciences, School of Public Health, University at Albany, Rensselaer, New York 12144, USA.

We investigated the mechanisms whereby omega-3 and -6 polyunsaturated fatty acids (PUFAs) cause cell death of mouse thymocytes using flow cytometry, focusing on the respective roles of intracellular calcium concentration, [Ca(2+)](i) and reactive oxygen species (ROS). We applied the C-22, 20, and 18 carbon omega-3 (DHA, EPA, ALA) and omega-6 (DTA, ARA, and LNA) fatty acids to isolated thymocytes and monitored cell death using the DNA-binding dye, propidium iodide. When applied at 20 µM concentration, omega-3 fatty acids killed thymocytes over a period of 1 h with a potency of DHA > EPA > ALA. The omega-6 PUFAs were more potent. The C18 omega-6 fatty acid, LNA, was the most potent, followed by DHA and ARA. Cell death was always accompanied by an increase in the levels of [Ca(2+)](i) and ROS. Both increases were in proportion to the potency of the PUFAs in inducing cell death. Removing extracellular calcium did not prevent the elevation in [Ca(2+)](i) nor cell death. However, the intracellular calcium chelator, BAPTA, almost totally reduced both the elevation in [Ca(2+)](i) and cell death, while vitamin E reduced the elevation in ROS and cell death. BAPTA also prevented the elevation in ROS, but vitamin E did not prevent the elevation in [Ca(2+)](i). Thapsigargin, which depletes endoplasmic reticulum calcium, blocked the elevation in [Ca(2+)](i), but CCCP, a mitochondrial calcium uptake inhibitor, did not. These results suggest that the six PUFAs we studied kill thymocytes by causing release of calcium from endoplasmic reticulum, which causes release of ROS from mitochondria which leads to cell death.
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http://dx.doi.org/10.1002/jcp.22290DOI Listing
November 2010

Functional impact of global rare copy number variation in autism spectrum disorders.

Nature 2010 Jul 9;466(7304):368-72. Epub 2010 Jun 9.

The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.

The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 x 10(-4)). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
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http://dx.doi.org/10.1038/nature09146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3021798PMC
July 2010

A 2cM genome-wide scan of European Holstein cattle affected by classical BSE.

BMC Genet 2010 Mar 29;11:20. Epub 2010 Mar 29.

Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.

Background: Classical bovine spongiform encephalopathy (BSE) is an acquired prion disease that is invariably fatal in cattle and has been implicated as a significant human health risk. Polymorphisms that alter the prion protein of sheep or humans have been associated with variations in transmissible spongiform encephalopathy susceptibility or resistance. In contrast, there is no strong evidence that non-synonymous mutations in the bovine prion gene (PRNP) are associated with classical BSE disease susceptibility. However, two bovine PRNP insertion/deletion polymorphisms, one within the promoter region and the other in intron 1, have been associated with susceptibility to classical BSE. These associations do not explain the full extent of BSE susceptibility, and loci outside of PRNP appear to be associated with disease incidence in some cattle populations. To test for associations with BSE susceptibility, we conducted a genome wide scan using a panel of 3,072 single nucleotide polymorphism (SNP) markers on 814 animals representing cases and control Holstein cattle from the United Kingdom BSE epidemic.

Results: Two sets of BSE affected Holstein cattle were analyzed in this study, one set with known family relationships and the second set of paired cases with controls. The family set comprises half-sibling progeny from six sires. The progeny from four of these sires had previously been scanned with microsatellite markers. The results obtained from the current analysis of the family set yielded both some supporting and new results compared with those obtained in the earlier study. The results revealed 27 SNPs representing 18 chromosomes associated with incidence of BSE disease. These results confirm a region previously reported on chromosome 20, and identify additional regions on chromosomes 2, 14, 16, 21 and 28. This study did not identify a significant association near the PRNP in the family sample set. The only association found in the PRNP region was in the case-control sample set and this was not significant after multiple test correction. The genome scan of the case-control animals did not identify any associations that passed a stringent genome-wide significance threshold.

Conclusions: Several regions of the genome are statistically associated with the incidence of classical BSE in European Holstein cattle. Further investigation of loci on chromosomes 2, 14, 16, 20, 21 and 28 will be required to uncover any biological significance underlying these marker associations.
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http://dx.doi.org/10.1186/1471-2156-11-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853485PMC
March 2010

A first generation whole genome RH map of the river buffalo with comparison to domestic cattle.

BMC Genomics 2008 Dec 24;9:631. Epub 2008 Dec 24.

Department of Biologia, UNESP - São Paulo State University, IBILCE, SP, Brazil.

Background: The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species.

Results: A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD >or= 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score >or= 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0).

Conclusion: We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.
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http://dx.doi.org/10.1186/1471-2164-9-631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2625372PMC
December 2008

High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly.

BMC Genomics 2007 Sep 4;8:310. Epub 2007 Sep 4.

Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton T6G2P5, Alberta, Canada.

Background: High resolution radiation hybrid (RH) maps can facilitate genome sequence assembly by correctly ordering genes and genetic markers along chromosomes. The objective of the present study was to generate high resolution RH maps of bovine chromosomes 19 (BTA19) and 29 (BTA29), and compare them with the current 7.1X bovine genome sequence assembly (bovine build 3.1). We have chosen BTA19 and 29 as candidate chromosomes for mapping, since many Quantitative Trait Loci (QTL) for the traits of carcass merit and residual feed intake have been identified on these chromosomes.

Results: We have constructed high resolution maps of BTA19 and BTA29 consisting of 555 and 253 Single Nucleotide Polymorphism (SNP) markers respectively using a 12,000 rad whole genome RH panel. With these markers, the RH map of BTA19 and BTA29 extended to 4591.4 cR and 2884.1 cR in length respectively. When aligned with the current bovine build 3.1, the order of markers on the RH map for BTA19 and 29 showed inconsistencies with respect to the genome assembly. Maps of both the chromosomes show that there is a significant internal rearrangement of the markers involving displacement, inversion and flips within the scaffolds with some scaffolds being misplaced in the genome assembly. We also constructed cattle-human comparative maps of these chromosomes which showed an overall agreement with the comparative maps published previously. However, minor discrepancies in the orientation of few homologous synteny blocks were observed.

Conclusion: The high resolution maps of BTA19 (average 1 locus/139 kb) and BTA29 (average 1 locus/208 kb) presented in this study suggest that by the incorporation of RH mapping information, the current bovine genome sequence assembly can be significantly improved. Furthermore, these maps can serve as a potential resource for fine mapping QTL and identification of causative mutations underlying QTL for economically important traits.
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http://dx.doi.org/10.1186/1471-2164-8-310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2064936PMC
September 2007