Publications by authors named "Anshika Srivastava"

35 Publications

The major genetic risk factor for severe COVID-19 does not show any association among South Asian populations.

Sci Rep 2021 06 11;11(1):12346. Epub 2021 Jun 11.

Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.

With the growing evidence on the variable human susceptibility against COVID-19, it is evident that some genetic loci modulate the severity of the infection. Recent studies have identified several loci associated with greater severity. More recently, a study has identified a 50 kb genomic segment introgressed from Neanderthal adding a risk for COVID-19, and this genomic segment is present among 16% and 50% people of European and South Asian descent, respectively. Our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations, respectively, which appears to be responsible for the low case fatality rate among South Asian populations. This result was also consistent with the real-time infection rate and case fatality rate among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the real-time infection rates and case fatality rate in India. We found that the polymorphism present in the 50 kb introgressed genomic segment (rs10490770) did not show any significant correlation with the infection and case fatality rate in India.
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http://dx.doi.org/10.1038/s41598-021-91711-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196069PMC
June 2021

An innovative technique for electronic transport model of group-III nitrides.

Sci Rep 2020 Oct 30;10(1):18706. Epub 2020 Oct 30.

Department of Physics, University of Lucknow, Lucknow, 226007, India.

An optimized empirical pseudopotential method (EPM) in conjunction with virtual crystal approximation (VCA) and the compositional disorder effect is used for simulation to extract the electronic material parameters of wurtzite nitride alloys to ensure excellent agreement with the experiments. The proposed direct bandgap results of group-III nitride alloys are also compared with the different density functional theories (DFT) based theoretical results. The model developed in current work, significantly improves the accuracy of calculated band gaps as compared to the ab-initio method based results. The physics of carrier transport in binary and ternary nitride materials is investigated with the help of in-house developed Monte Carlo algorithms for solution of Boltzmann transport equation (BTE) including nonlinear scattering mechanisms. Carrier-carrier scattering mechanisms defined through Coulomb-, piezoelectric-, ionized impurity-, surface roughness-scattering with acoustic and intervalley scatterings, all have been given due consideration in present model. The direct and indirect energy bandgap results have been calibrated with the experimental data and use of symmetric and asymmetric form factors associated with respective materials. The electron mobility results of each binary nitride material have been compared and contrasted with experimental results under appropriate conditions and good agreement has been found between simulated and experimental results.
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http://dx.doi.org/10.1038/s41598-020-75588-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603329PMC
October 2020

Genetic Association of rs2285666 Polymorphism With COVID-19 Spatial Distribution in India.

Front Genet 2020 25;11:564741. Epub 2020 Sep 25.

Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India.

Studies on host-pathogen interaction have identified human ACE2 as a host cell receptor responsible for mediating infection by coronavirus (COVID-19). Subsequent studies have shown striking difference of allele frequency among Europeans and Asians for a polymorphism rs2285666, present in . It has been revealed that the alternate allele (TT-plus strand or AA-minus strand) of rs2285666 elevate the expression level of this gene upto 50%, hence may play a significant role in SARS-CoV-2 susceptibility. Therefore, we have first looked the phylogenetic structure of rs2285666 derived haplotypes in worldwide populations and compared the spatial frequency of this particular allele with respect to the COVID-19 infection as well as case-fatality rate in India. For the first time, we ascertained a significant positive correlation for alternate allele (T or A) of rs2285666, with the lower infection as well as case-fatality rate among Indian populations. We trust that this information will be useful to understand the role of in COVID-19 susceptibility.
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http://dx.doi.org/10.3389/fgene.2020.564741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545580PMC
September 2020

Most frequent South Asian haplotypes of ACE2 share identity by descent with East Eurasian populations.

PLoS One 2020 16;15(9):e0238255. Epub 2020 Sep 16.

Department of Zoology, Cytogenetics Laboratory, Banaras Hindu University, Varanasi, India.

It was shown that the human Angiotensin-converting enzyme 2 (ACE2) is the receptor of recent coronavirus SARS-CoV-2, and variation in this gene may affect the susceptibility of a population. Therefore, we have analysed the sequence data of ACE2 among 393 samples worldwide, focusing on South Asia. Genetically, South Asians are more related to West Eurasian populations rather than to East Eurasians. In the present analyses of ACE2, we observed that the majority of South Asian haplotypes are closer to East Eurasians rather than to West Eurasians. The phylogenetic analysis suggested that the South Asian haplotypes shared with East Eurasians involved two unique event polymorphisms (rs4646120 and rs2285666). In contrast with the European/American populations, both of the SNPs have largely similar frequencies for East Eurasians and South Asians, Therefore, it is likely that among the South Asians, host susceptibility to the novel coronavirus SARS-CoV-2 will be more similar to that of East Eurasians rather than to that of Europeans.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0238255PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494073PMC
September 2020

Genetic and linguistic non-correspondence suggests evidence for collective social climbing in the Kol tribe of South Asia.

Sci Rep 2020 03 27;10(1):5593. Epub 2020 Mar 27.

Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.

Both classical and recent genetic studies have unanimously concluded that the genetic landscape of South Asia is unique. At long distances the 'isolation-by-distance' model appears to correspond well with the genetic data, whereas at short distances several other factors, including the caste, have been shown to be strong determinant factors. In addition with these, tribal populations speaking various languages add yet another layer of genetic complexity. The Kol are the third most populous tribal population in India, comprising communities speaking Austroasiatic languages of the Northern Munda branch. Yet, the Kol have not hitherto undergone in-depth genetic analysis. In the present study, we have analysed two Kol groups of central and western India for hundreds thousands of autosomal and several mitochondrial DNA makers to infer their fine genetic structure and affinities to other Eurasian populations. In contrast, with their known linguistic affinity, the Kol share their more recent common ancestry with the Indo-European and Dravidian speaking populations. The geographic-genetic neighbour tests at both the temporal and spatial levels have suggested some degree of excess allele sharing of Kol1 with Kol2, thereby indicating their common stock. Our extensive analysis on the Kol ethnic group shows South Asia to be a living genetics lab, where real-time tests can be performed on existing hypotheses.
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http://dx.doi.org/10.1038/s41598-020-61941-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101412PMC
March 2020

Design and analysis of visible photonics resonators coated with CuO thin film.

Nanotechnology 2020 Apr 20;31(15):155201. Epub 2019 Dec 20.

Department of Electronics & Communication Engineering, Motilal Nehru National Institute of Technology Allahabad, Prayagraj-211004, India.

The optical and structural properties of CuO film deposited on n-Si via spin-coating method have been ascertained for diverse annealing times. The characterizations were made using x-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), UV-vis spectroscopy, ellipsometry spectroscopy and photoluminescence. A detailed analysis revealed the favorable behavior of CuO film for visible photonics resonators such as Fabry-Perot (FP) and ring resonators. The best suitable property was obtained for a film annealed for 15 min. Accordingly, the CuO-film-coated resonators were simulated and analyzed theoretically using the MODE Solutions tool by Lumerical and MATLAB. In the FP resonator, the transmission intensity, contrast factor and finesse were computed for different annealing times and angles of light incidence. Further, for the CuO ring resonator, an eigenmode solver was incorporated (in the wavelength range 300-900 nm) to compute the effective refractive index, propagation constant, group velocity, losses, dispersion and transmission intensity. Additionally, utilizing the basic expressions, the free spectral range, full-width at half-maximum and quality factor were derived.
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http://dx.doi.org/10.1088/1361-6528/ab6469DOI Listing
April 2020

Historic migration to South Asia in the last two millennia: A case of Jewish and Parsi populations.

J Biosci 2019 Jul;44(3)

Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, Tartu 51010, Estonia.

The South Asian populations have a mosaic of ancestries likely due to the interactions of long-term populations of the landmass and those of East andWest Eurasia. Apart from prehistoric dispersals, there are some known population movements to India. In this study,we focussed on the migration of Jewish and Parsi populations on temporal and spatial scales. The existence of Jewish and Parsi communities in India are recorded since ancient times. However, due to the lack of high-resolution genetic data, their origin and affiliation with other Indian and non-Indian populations remains shrouded in legends. Earlier genetic studies on populations of Indian Jews have found evidence for a minor shared ancestry of Indian Jews with Middle Eastern (Jews) populations, whereas for Parsis, the Iranian link was proposed. Recently, in our high-resolution study, we were able to quantify the admixture dynamics of these groups, which has suggested a male-biased admixture. Here, we added the newly available ancient samples and revisited the interplay of genes and cultures. Thus, in this study we reconstructed a broad genetic profile of Indian Jews and Parsis to paint a fine-grained picture of these ethnic groups.
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July 2019

The peopling of Lakshadweep Archipelago.

Sci Rep 2019 05 6;9(1):6968. Epub 2019 May 6.

CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.

The archipelago of Lakshadweep is considered as a stopover to the maritime route since ancient time. It is not very clear when the human first occupied these islands, however in the long history of the islands, the local legends suggest that Lakshadweep has been ruled by different kingdoms. To have a better understanding of peopling of Lakshadweep, we have analysed 557 individuals from eight major islands for mitochondrial DNA and 166 individuals for Y chromosome markers. We found a strong founder effect for both paternal and maternal lineages. Moreover, we report a close genetic link of Lakshadweep islanders with the Maldives, Sri Lanka and India. Most of the Lakshadweep islands share the haplogroups specific to South Asia and West Eurasia, except Minicoy Island that also shares haplogroups of East Eurasia. The paternal and maternal ancestries of the majority of island populations suggest their arrival from distinct sources. We found that the maternal ancestry was closer to South Indian populations, whereas the paternal ancestry was overwhelmed with the haplogroups, more common in the Maldives and North of India. In conclusion, our first genetic data suggest that the majority of human ancestry in Lakshadweep is largely derived from South Asia with minor influences from East and West Eurasia.
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http://dx.doi.org/10.1038/s41598-019-43384-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6502849PMC
May 2019

Photosensitivity and type I IFN responses in cutaneous lupus are driven by epidermal-derived interferon kappa.

Ann Rheum Dis 2018 11 18;77(11):1653-1664. Epub 2018 Jul 18.

Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.

Objective: Skin inflammation and photosensitivity are common in patients with cutaneous lupus erythematosus (CLE) and systemic lupus erythematosus (SLE), yet little is known about the mechanisms that regulate these traits. Here we investigate the role of interferon kappa (IFN-κ) in regulation of type I interferon (IFN) and photosensitive responses and examine its dysregulation in lupus skin.

Methods: mRNA expression of type I IFN genes was analysed from microarray data of CLE lesions and healthy control skin. Similar expression in cultured primary keratinocytes, fibroblasts and endothelial cells was analysed via RNA-seq. knock-out (KO) keratinocytes were generated using CRISPR/Cas9. Keratinocytes stably overexpressing IFN-κ were created via G418 selection of transfected cells. IFN responses were assessed via phosphorylation of STAT1 and STAT2 and qRT-PCR for IFN-regulated genes. Ultraviolet B-mediated apoptosis was analysed via TUNEL staining. In vivo protein expression was assessed via immunofluorescent staining of normal and CLE lesional skin.

Results: is one of two type I IFNs significantly increased (1.5-fold change, false discovery rate (FDR) q<0.001) in lesional CLE skin. Gene ontology (GO) analysis showed that type I IFN responses were enriched (FDR=6.8×10) in keratinocytes not in fibroblast and endothelial cells, and this epithelial-derived IFN-κ is responsible for maintaining baseline type I IFN responses in healthy skin. Increased levels of IFN-κ, such as seen in SLE, amplify and accelerate responsiveness of epithelia to IFN-α and increase keratinocyte sensitivity to UV irradiation. Notably, KO of IFN-κ or inhibition of IFN signalling with baricitinib abrogates UVB-induced apoptosis.

Conclusion: Collectively, our data identify IFN-κ as a critical IFN in CLE pathology via promotion of enhanced IFN responses and photosensitivity. IFN-κ is a potential novel target for UVB prophylaxis and CLE-directed therapy.
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http://dx.doi.org/10.1136/annrheumdis-2018-213197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6185784PMC
November 2018

Genetic diversity of NDUFV1-dependent mitochondrial complex I deficiency.

Eur J Hum Genet 2018 11 5;26(11):1582-1587. Epub 2018 Jul 5.

Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA.

Medical genomics research performed in diverse population facilitates a better understanding of the genetic basis of developmental disorders, with regional implications for community genetics. Autosomal recessive mitochondrial complex I deficiency (MCID) accounts for a constellation of clinical features, including encephalopathies, myopathies, and Leigh Syndrome. Using whole-exome sequencing, we identified biallelic missense variants in NDUFV1 that encodes the 51-kD subunit of complex I (NADH dehydrogenase) NDUFV1. Mapping the variants on published crystal structures of mitochondrial complex I demonstrate that the novel c.1118T > C (p.(Phe373Ser)) variant is predicted to diminish the affinity of the active pocket of NDUFV1 for FMN that correlates to an early onset of debilitating MCID symptoms. The c.1156C > T (p.(Arg386Cys)) variant is predicted to alter electron shuttling required for energy production and correlate to a disease onset in childhood. NDUFV1 c.1156C > T (p.(Arg386Cys)) represents a founder variant in South Asian populations that have value in prioritizing this variant in a population-specific manner for genetic diagnostic evaluation. In conclusion, our results demonstrate the advantage of analyzing population-specific sequences to understand the disease pathophysiology and prevalence of inherited risk variants in the underrepresented populations.
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http://dx.doi.org/10.1038/s41431-018-0209-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6189076PMC
November 2018

Report of four novel variants in ASNS causing asparagine synthetase deficiency and review of literature.

Congenit Anom (Kyoto) 2018 Sep 20;58(5):181-182. Epub 2018 Feb 20.

Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.

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http://dx.doi.org/10.1111/cga.12275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338226PMC
September 2018

Genotype-phenotype correlations in individuals with pathogenic RERE variants.

Hum Mutat 2018 05 25;39(5):666-675. Epub 2018 Jan 25.

Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas.

Heterozygous variants in the arginine-glutamic acid dipeptide repeats gene (RERE) have been shown to cause neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH). Here, we report nine individuals with NEDBEH who carry partial deletions or deleterious sequence variants in RERE. These variants were found to be de novo in all cases in which parental samples were available. An analysis of data from individuals with NEDBEH suggests that point mutations affecting the Atrophin-1 domain of RERE are associated with an increased risk of structural eye defects, congenital heart defects, renal anomalies, and sensorineural hearing loss when compared with loss-of-function variants that are likely to lead to haploinsufficiency. A high percentage of RERE pathogenic variants affect a histidine-rich region in the Atrophin-1 domain. We have also identified a recurrent two-amino-acid duplication in this region that is associated with the development of a CHARGE syndrome-like phenotype. We conclude that mutations affecting RERE result in a spectrum of clinical phenotypes. Genotype-phenotype correlations exist and can be used to guide medical decision making. Consideration should also be given to screening for RERE variants in individuals who fulfill diagnostic criteria for CHARGE syndrome but do not carry pathogenic variants in CHD7.
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http://dx.doi.org/10.1002/humu.23400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5903952PMC
May 2018

Dysregulation of cotranscriptional alternative splicing underlies CHARGE syndrome.

Proc Natl Acad Sci U S A 2018 01 8;115(4):E620-E629. Epub 2018 Jan 8.

Molecular Genetics of Development Laboratory, Department of Biological Sciences, University of Quebec at Montreal, Montreal, QC H2X 3Y7, Canada;

CHARGE syndrome-which stands for coloboma of the eye, heart defects, atresia of choanae, retardation of growth/development, genital abnormalities, and ear anomalies-is a severe developmental disorder with wide phenotypic variability, caused mainly by mutations in (chromodomain helicase DNA-binding protein 7), known to encode a chromatin remodeler. The genetic lesions responsible for mutation-negative cases are unknown, at least in part because the pathogenic mechanisms underlying CHARGE syndrome remain poorly defined. Here, we report the characterization of a mouse model for mutation-negative cases of CHARGE syndrome generated by insertional mutagenesis of (family with sequence similarity 172, member A). We show that Fam172a plays a key role in the regulation of cotranscriptional alternative splicing, notably by interacting with Ago2 (Argonaute-2) and Chd7. Validation studies in a human cohort allow us to propose that dysregulation of cotranscriptional alternative splicing is a unifying pathogenic mechanism for both mutation-positive and mutation-negative cases. We also present evidence that such splicing defects can be corrected in vitro by acute rapamycin treatment.
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http://dx.doi.org/10.1073/pnas.1715378115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789929PMC
January 2018

Genetic analysis of CHARGE syndrome identifies overlapping molecular biology.

Genet Med 2018 09 4;20(9):1022-1029. Epub 2018 Jan 4.

Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA.

Purpose: CHARGE syndrome is an autosomal-dominant, multiple congenital anomaly condition characterized by vision and hearing loss, congenital heart disease, and malformations of craniofacial and other structures. Pathogenic variants in CHD7, encoding adenosine triphosphate-dependent chromodomain helicase DNA binding protein 7, are present in the majority of affected individuals. However, no causal variant can be found in 5-30% (depending on the cohort) of individuals with a clinical diagnosis of CHARGE syndrome.

Methods: We performed whole-exome sequencing (WES) on 28 families from which at least one individual presented with features highly suggestive of CHARGE syndrome.

Results: Pathogenic variants in CHD7 were present in 15 of 28 individuals (53.6%), whereas 4 (14.3%) individuals had pathogenic variants in other genes (RERE, KMT2D, EP300, or PUF60). A variant of uncertain clinical significance in KDM6A was identified in one (3.5%) individual. The remaining eight (28.6%) individuals were not found to have pathogenic variants by WES.

Conclusion: These results demonstrate that the phenotypic features of CHARGE syndrome overlap with multiple other rare single-gene syndromes. Additionally, they implicate a shared molecular pathology that disrupts epigenetic regulation of multiple-organ development.
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http://dx.doi.org/10.1038/gim.2017.233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6034995PMC
September 2018

Homozygous c.359del variant in MGME1 is associated with early onset cerebellar ataxia.

Eur J Med Genet 2017 Oct 12;60(10):533-535. Epub 2017 Jul 12.

Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India. Electronic address:

We ascertained a child with early onset cerebellar ataxia and identified a novel frameshift deletion, c.359del [p. (Pro120Leufs*2), NM_052865.2] in exon 2 of MGME1 (mitochondrial genome maintenance exonuclease 1) by exome sequencing. Variations in MGME1 have been reported to cause mitochondrial DNA (mtDNA) depletion syndrome 11 (MIM #615084) in an earlier work. The phenotype included progressive external ophthalmoplegia, emaciation, respiratory failure and late onset progressive ataxia. However, the child presented here has early onset progressive ataxia, speech delay, microcephaly, cerebellar atrophy and fundus albipunctatus. This is the second report of a mutation in MGME1 and describes a more severe phenotype.
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http://dx.doi.org/10.1016/j.ejmg.2017.07.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379073PMC
October 2017

Histone H2A Monoubiquitination in Neurodevelopmental Disorders.

Trends Genet 2017 08 29;33(8):566-578. Epub 2017 Jun 29.

Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA; Cell and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA. Electronic address:

Covalent histone modifications play an essential role in gene regulation and cellular specification required for multicellular organism development. Monoubiquitination of histone H2A (H2AUb1) is a reversible transcriptionally repressive mark. Exchange of histone H2A monoubiquitination and deubiquitination reflects the succession of transcriptional profiles during development required to produce cellular diversity from pluripotent cells. Germ-line pathogenic variants in components of the H2AUb1 regulatory axis are being identified as the genetic basis of congenital neurodevelopmental disorders. Here, we review the human genetics findings coalescing on molecular mechanisms that alter the genome-wide distribution of this histone modification required for development.
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http://dx.doi.org/10.1016/j.tig.2017.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5562288PMC
August 2017

Homozygous p.(Glu87Lys) variant in ISCA1 is associated with a multiple mitochondrial dysfunctions syndrome.

J Hum Genet 2017 Jul 30;62(7):723-727. Epub 2017 Mar 30.

Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India.

The iron-sulfur (Fe-S) cluster (ISC) biogenesis pathway is indispensable for many fundamental biological processes and pathogenic variations in genes encoding several components of the Fe-S biogenesis machinery, such as NFU1, BOLA3, IBA57 and ISCA2 are already implicated in causing four types of multiple mitochondrial dysfunctions syndromes (MMDS). We report on two unrelated families, with two affected children each with early onset neurological deterioration, seizures, extensive white matter abnormalities, cortical migrational abnormalities, lactic acidosis and early demise. Exome sequencing of two affected individuals, one from each family, revealed a homozygous c.259G>A [p.(Glu87Lys)] variant in ISCA1 and Mendelian segregation was confirmed in both families. The ISCA1 variant lies in the only shared region of homozygosity between the two families suggesting the possibility of a founder effect. In silico functional analyses and structural modeling of the protein predict the identified ISCA1 variant to be detrimental to protein stability and function. Notably the phenotype observed in all affected subjects with the ISCA1 pathogenic variant is similar to that previously described in all four types of MMDS. Our findings suggest association of a pathogenic variant in ISCA1 with another MMDS.
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http://dx.doi.org/10.1038/jhg.2017.35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484744PMC
July 2017

Role of common sarcomeric gene polymorphisms in genetic susceptibility to left ventricular dysfunction.

J Genet 2016 Jun;95(2):263-72

Department of Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226 014, India.

Mutations in sarcomeric genes are common genetic cause of cardiomyopathies. An intronic 25-bp deletion in cardiac myosin binding protein C (MYBPC3) at 3' region is associated with dilated and hypertrophic cardiomyopathies in Southeast Asia. However, the frequency of sarcomeric gene polymorphisms and associated clinical presentation have not been established with left ventricular dysfunction (LVD). Therefore, the aim of the present study was to explore the association of MYBPC3 25-bp deletion, titin (TTN) 18 bp I/D, troponin T type 2 (TNNT2) 5 bp I/D and myospryn K2906N polymorphisms with LVD. This study includes 988 consecutive patients with angiographically confirmed coronary artery disease (CAD) and 300 healthy controls. Among the 988 CAD patients, 253 with reduced left ventricle ejection fraction (LVEF≤45%) were categorized as LVD. MYBPC3 25-bp deletion, TTN 18 bp I/D and TNNT2 5 bp I/D polymorphisms were determined by direct polymerase chain reaction method, while myospryn K2906N polymorphism by TaqMan assay. Our results showed that MYBPC3 25-bp deletion polymorphism was significantly associated with elevated risk of LVD (LVEF <45) (healthy controls versus LVD: OR=3.85, P <0.001; and nonLVD versus LVD: OR=1.65, P = 0.035), while TTN 18 bp I/D, TNNT2 5 bp I/D and myospryn K2906N polymorphisms did not show any significant association with LVD. The results also showed that MYBPC3 25-bp deletion polymorphism was significantly associated with other parameters of LV remodelling, i.e. LV dimensions (LV end diastole dimension, LVEDD: P = 0.037 and LV end systolic dimension, LVESD: P = 0.032). Our data suggests that MYBPC3 25-bp deletion may play significant role in conferring LVD as well as CAD risk in north Indian population.
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http://dx.doi.org/10.1007/s12041-016-0623-4DOI Listing
June 2016

De novo dominant ASXL3 mutations alter H2A deubiquitination and transcription in Bainbridge-Ropers syndrome.

Hum Mol Genet 2016 Feb 8;25(3):597-608. Epub 2015 Dec 8.

Department of Human Genetics,

De novo truncating mutations in Additional sex combs-like 3 (ASXL3) have been identified in individuals with Bainbridge-Ropers syndrome (BRS), characterized by failure to thrive, global developmental delay, feeding problems, hypotonia, dysmorphic features, profound speech delays and intellectual disability. We identified three novel de novo heterozygous truncating variants distributed across ASXL3, outside the original cluster of ASXL3 mutations previously described for BRS. Primary skin fibroblasts established from a BRS patient were used to investigate the functional impact of pathogenic variants. ASXL3 mRNA transcripts from the mutated allele are prone to nonsense-mediated decay, and expression of ASXL3 is reduced. We found that ASXL3 interacts with BAP1, a hydrolase that removes mono-ubiquitin from histone H2A lysine 119 (H2AK119Ub1) as a component of the Polycomb repressive deubiquitination (PR-DUB) complex. A significant increase in H2AK119Ub1 was observed in ASXL3 patient fibroblasts, highlighting an important functional role for ASXL3 in PR-DUB mediated deubiquitination. Transcriptomes of ASXL3 patient and control fibroblasts were compared to investigate the impact of chromatin changes on transcriptional regulation. Out of 564 significantly differentially expressed genes (DEGs) in ASXL3 patient fibroblasts, 52% were upregulated and 48% downregulated. DEGs were enriched in molecular processes impacting transcriptional regulation, development and proliferation, consistent with the features of BRS. This is the first single gene disorder linked to defects in deubiquitination of H2AK119Ub1 and suggests an important role for dynamic regulation of H2A mono-ubiquitination in transcriptional regulation and the pathophysiology of BRS.
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http://dx.doi.org/10.1093/hmg/ddv499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731023PMC
February 2016

Role of angiotensin II type I (AT1 A1166C) receptor polymorphism in susceptibility of left ventricular dysfunction.

Indian Heart J 2015 May-Jun;67(3):214-21. Epub 2015 May 7.

Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, UP, India. Electronic address:

Background: Left ventricular dysfunction (LVD) with subsequent congestive heart failure (CHF) constitutes the final common pathway for a host of cardiac disorders. The impaired LV function develops in response to an ischemic insult followed by a fall in cardiac output that leads to activation of renin-angiotensin-system (RAS). Angiotensin II type I receptor (AT1), which mediate the vasoconstrictive and salt-conserving actions of the RAS, represent interesting candidate genes for cardiovascular diseases. Therefore, we conducted an association study between single nucleotide polymorphism (SNP) in AT1 gene and LVD in CAD patients.

Methods And Results: The present study recruited a total of 950 subjects including 720 angiography confirmed CAD patients and 230 healthy controls. Among 720 CAD patients, 229 with reduced left ventricle ejection fraction (LVEF≤45%) were categorized as LVD. The AT1 (A1166C, rs5186) polymorphism was determined by ARMS-PCR. Our results showed that the frequency of AT1 1166AC and CC genotypes were significantly higher in LVD patients in comparison to non-LVD (LVEF >45%) patients (p value = 0.003; OR = 1.81 and p value <0.001; OR = 4.33). Further analysis showed that AT1 A1166C polymorphism was significantly associated with LV end diastole (p-value = 0.031), end systole (p-value = 0.038) dimensions, and mean LVEF (p-value = 0.035). Moreover, on comparing the AT1 A1166C polymorphism in CAD patients with healthy controls, we did not find any association both at genotypic and allelic level (p value = 0.927; OR = 1.04 and p value = 0.219; OR = 0.83) respectively.

Conclusions: Our study suggests that AT1 A1166C polymorphism may play significant role in conferring genetic susceptibility of LVD.
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http://dx.doi.org/10.1016/j.ihj.2015.04.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495590PMC
December 2016

Matrix metalloproteinases in coronary artery disease.

Adv Clin Chem 2014 ;64:1-72

Matrix metalloproteinases (MMP) are a family of zinc-containing endoproteinases that degrade extracellular matrix (ECM) components. MMP have important roles in the development, physiology and pathology of cardiovascular system. Metalloproteases also play key roles in adverse cardiovascular remodeling, atherosclerotic plaque formation and plaque instability, vascular smooth muscle cell (SMC) migration and restenosis that lead to coronary artery disease (CAD), and progressive heart failure. The study of MMP in developing animal model cardiovascular systems has been helpful in deciphering numerous pathologic conditions in humans. Increased peripheral blood MMP-2 and MMP-9 in acute coronary syndrome (ACS) may be useful as noninvasive tests for detection of plaque vulnerability. MMP function can be modulated by certain pharmacological drugs that can be exploited for treatment of ACS. CAD is a polygenic disease and hundreds of genes contribute toward its predisposition. A large number of sequence variations in MMP genes have been identified. Case-control association studies have highlighted their potential association with CAD and its clinical manifestations. Although results thus far are inconsistent, meta-analysis has demonstrated that MMP-3 Glu45Lys and MMP-9 1562C/T gene polymorphisms were associated with CAD risk.
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http://dx.doi.org/10.1016/b978-0-12-800263-6.00001-xDOI Listing
August 2014

Genetic predisposition to left ventricular dysfunction: a multigenic and multi-analytical approach.

Gene 2014 Aug 27;546(2):309-17. Epub 2014 May 27.

Department of Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, UP, India. Electronic address:

Background: Left ventricular dysfunction (LVD) is a complex, multifactorial condition, caused by mechanical, neurohormonal, and genetic factors. We have previously observed association of renin-angiotensin-aldosterone system (RAAS), matrix metalloproteinases (MMPs) and inflammatory pathway genes with LVD. Therefore the present study was undertaken to identify the combination of genetic variants and their possible interactions contributing towards genetic susceptibility to LVD in the background of coronary artery disease (CAD).

Methods And Results: The study included 230 healthy controls and 510 consecutive patients with angiographically confirmed CAD. Among them, 162 with reduced left ventricle ejection fraction (LVEF≤45%) were categorized as having LVD. We analyzed 11 polymorphisms of RAAS, MMPs and inflammatory pathways. Single locus analysis showed that AT1 A1166C (p value<0.001; OR=3.67), MMP9 R668Q (p value=0.007; OR=3.48) and NFKB1-94 ATTG ins/del (p value=0.013; OR=2.01) polymorphisms were independently associated with LVD when compared with both non-LVD patients and healthy controls. High-order gene-gene interaction analysis, using classification and regression tree (CART) and multifactor dimensionality reduction (MDR) revealed that AT1 A1166C and NFKB1-94 ATTG ins/del polymorphisms jointly increased the risk of LVD to great extent (p-value=0.001; OR=8.55) and best four-factor interaction model consisted of AT1 A1166C, MMP7 A-181G, MMP9 R668Q and NFKB1-94 ATTG ins/del polymorphisms with testing accuracy of 0.566 and cross validation consistency (CVC)=9/10 (permutation p<0.001) showed increased risk for LVD respectively.

Conclusion: AT1 A1166C independently and in combination with MMP9 R668Q and NFKB1-94 ATTG ins/del polymorphisms plays important role in conferring genetic susceptibility to LVD in CAD patients.
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http://dx.doi.org/10.1016/j.gene.2014.05.060DOI Listing
August 2014

A multigenic approach to evaluate genetic variants of PLCE1, LXRs, MMPs, TIMP, and CYP genes in gallbladder cancer predisposition.

Tumour Biol 2014 Sep 27;35(9):8597-606. Epub 2014 May 27.

Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow, Uttar Pradesh, 226014, India,

Gallbladder cancer (GBC) is a violent neoplasm associated with late diagnosis, unsatisfactory treatment, and poor prognosis. The disease shows complex interplay between multiple genetic variants. We analyzed 15 polymorphisms in nine genes involved in various pathways to find out combinations of genetic variants contributing to GBC risk. The genes included in the study were matrix metalloproteinases (MMP-2, MMP-7, and MMP-9), tissue inhibitor of metalloproteinases (TIMP-2), cytochrome P450 (CYP)1A1, CYP1B1, phospholipase C epsilon 1 (PLCE1), liver X receptor (LXR)-alpha, and LXR-beta. Genotypes were determined by PCR-RFLP and TaqMan probes. Statistical analysis was done by SPSS version 16. Multilocus analysis was performed by Classification and Regression Tree (CART) analysis and multifactor dimensionality reduction (MDR) to gene-gene interactions in modifying GBC risk. In silico analysis was done using various bioinformatics tools (F-SNP, FAST-SNP). Single locus analysis showed association of MMP-2 (-735 C > T, -1306 C > T), MMP-7 - 181 A > G, MMP-9 (P574R, R668Q), TIMP-2 - 418 G > C, CYP1A1-MspI, CYP1A1-Ile462Val, PLCE1 (rs2274223 A > G, rs7922612 T > C) and LXR-beta T > C (rs3546355 G > A, rs2695121 T > C) polymorphisms with GBC risk (p < 0.05) whereas CYP1B1 and LXR-α variants were not associated with GBC risk. Multidimensional reduction analysis revealed LXR-β (rs3546355 G > A, rs2695121 T > C), MMP-2 (-1306 C > T), MMP-9 (R668Q), and PLCE1 rs2274223 A > G to be key players in GBC causation (p < 0.001, CVC = 7/10). The results were further supported by independent CART analysis (p < 0.001). In silico analysis of associated variants suggested change in splicing or transcriptional regulation. Interactome and STRING analysis showed network of associated genes. The study found PLCE1 and LXR-β network interactions as important contributory factors for genetic predisposition in gallbladder cancer.
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http://dx.doi.org/10.1007/s13277-014-2094-7DOI Listing
September 2014

Significant role of ADRB3 rs4994 towards the development of coronary artery disease.

Coron Artery Dis 2014 Jan;25(1):29-34

Departments of aGenetics bCardiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, Uttar Pradesh, India.

Background: Coronary artery disease (CAD) is the most common type of heart disease and cause of heart attacks. It has been proposed that both the susceptibility to disease and the interindividual variability in response to treatment relates in part to genetic polymorphisms, particularly those polymorphisms for neurotransmitter and drug receptors. Common functional polymorphisms in β-adrenergic receptor genes (ADRB) have been associated with heart failure phenotypes. Therefore, the purpose of the present study was to explore the association of genetic variants in ADRB3 (C190T or Trp64Arg) ADRB1 (C1165G or Arg389Gly), and ADRA2A (C-1291G) with CAD.

Materials And Methods: The present study recruited a total of 600 consecutive patients with angiographically confirmed CAD and 200 population-matched controls (173 men and 27 women) (mean age 54.10±8.30 years). The ADRB3 T190C, ADRA2A C-1291G, and ADRB1 C1165G polymorphisms were determined by PCR-restriction fragment length polymorphism. The putative functional effects were determined in the coding region of the ADRD3 gene by online web servers FASTSNP and F-SNP.

Results: On comparing the genotype frequency distribution in CAD patients with that of healthy individuals, significant association was observed with the CC genotype of the ADRB3 T190C polymorphism (P=0.040, odds ratio=1.5). Also, at the allelic level the C allele of ADRB3 T190C conferred risk for CAD (P=0.005, odds ratio=1.7). The ADRA2A C-1291G and ADRB1 C1165G polymorphisms were not found to be a risk for CAD when compared with controls.

Conclusion: The present study finding suggests that ADRB3 C190T may also be involved in the complex pathophysiology of CAD.
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http://dx.doi.org/10.1097/MCA.0000000000000056DOI Listing
January 2014

Multi-analytic approach elucidates significant role of hormonal and hepatocanalicular transporter genetic variants in gallstone disease in North Indian population.

PLoS One 2013 8;8(4):e59173. Epub 2013 Apr 8.

Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS) Lucknow, Uttar Pradesh, India.

Objective: Cholesterol gallstone disease (CGD) is a multifactorial and multistep disease. Apart from female gender and increasing age being the documented non-modifiable risk factor for gallstones the pathobiological mechanisms underlying the phenotypic expression of CGD appear to be rather complex, and one or more variations in genes could play critical roles in the diverse pathways further progressing to cholesterol crystal formation. In the present study we performed genotyping score, Multifactor dimensionality reduction (MDR) and Classification and Regression Tree analysis (CART) to identify combinations of alleles among the hormonal, hepatocanalicular transporter and adipogenesis differentiation pathway genes in modifying the risk for CGD.

Design: The present case-control study recruited total of 450 subjects, including 230 CGD patients and 220 controls. We analyzed common ESR1, ESR2, PGR, ADRB3, ADRA2A, ABCG8, SLCO1B1, PPARγ2, and SREBP2 gene polymorphisms to find out combinations of genetic variants contributing to CGD risk, using multi-analytical approaches (G-score, MDR, and CART).

Results: Single locus analysis by logistic regression showed association of ESR1 IVS1-397C>T (rs2234693), IVS1-351A>G (rs9340799) PGR ins/del (rs1042838) ADRB3-190 T>C (rs4994) ABCG8 D19H (rs11887534), SLCO1B1 Exon4 C>A (rs11045819) and SREBP2 1784G>C (rs2228314) with CGD risk. However, the MDR and CART analysis revealed ESR1 IVS1-397C>T (rs2234693) ADRB3-190 T>C (rs4994) and ABCG8 D19H (rs11887534) polymorphisms as the best polymorphic signature for discriminating between cases and controls. The overall odds ratio for the applied multi-analytical approaches ranged from 4.33 to 10.05 showing an incremental risk for cholesterol crystal formation. In conclusion, our muti-analytical approach suggests that, ESR1, ADRB3, in addition to ABCG8 genetic variants confer significant risk for cholesterol gallstone disease.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059173PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3620121PMC
October 2013

Role of inflammatory gene polymorphisms in left ventricular dysfunction (LVD) susceptibility in coronary artery disease (CAD) patients.

Cytokine 2013 Mar 26;61(3):856-61. Epub 2013 Jan 26.

Department of Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226 014 (UP), India.

Rationale: Inflammation exacerbates a number of deleterious effects on the heart, most notable being left ventricular dysfunction (LVD). A promoter polymorphism of the NFKB1 gene (encodes p50 subunit) results in lower protein levels of NFkB p50 subunits, which in its dimmer (p50) form has anti-inflammatory effects. The active NFkB transcription factor promotes the expression of over 150 target genes including IL6 and TNF-α. Therefore, the aim of the present study was to assess the association of NFKB1, IL6 and TNF-α gene polymorphisms with LVD in coronary artery disease (CAD) patients.

Methods And Results: The present study included a total of 830 subjects (600 CAD patients and 230 controls) and was carried out in two (primary and replication) cohorts. CAD patients with reduced left ventricle ejection fraction (LVEF ≤45%) were categorized having LVD. The NFKB1 -94 ATTG ins/del (rs28362491), IL6 -174 G/C (rs1800795) and TNF-α -308 G/A (rs1800629) polymorphisms were genotyped by PCR/ARMS-PCR methods. The results of the primary cohort were validated in a replicative cohort and pooled by meta-analysis using Fisher's and Mantel-Haenszel test. The analysis showed that NFKB1 ATTG/ATTG genotype was significantly associated with LVD (Fisher's method p-value=0.007, Mantel-Haenszel OR=2.34), LV end diastole (p-value=0.013), end systole (p-value=0.011) dimensions, LV mass (p-value=0.024), mean LVEF (p-value=0.001) and myocardial infarction (p-value=0.043).

Conclusion: Our data suggests that NFKB1 -94 ATTG ins/del polymorphism plays significant role in conferring susceptibility of LVD and ATTG/ATTG genotype may modulate risk of heart failure by increasing ventricular remodeling and worsening LV function.
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http://dx.doi.org/10.1016/j.cyto.2012.12.020DOI Listing
March 2013

Genetic and functional identification of the likely causative variant for cholesterol gallstone disease at the ABCG5/8 lithogenic locus.

Hepatology 2013 Jun 25;57(6):2407-17. Epub 2013 Jan 25.

Department of Internal Medicine I, Hospital Schleswig-Holstein, Kiel, Germany.

Unlabelled: The sterolin locus (ABCG5/ABCG8) confers susceptibility for cholesterol gallstone disease in humans. Both the responsible variant and the molecular mechanism causing an increased incidence of gallstones in these patients have as yet not been identified. Genetic mapping utilized patient samples from Germany (2,808 cases, 2,089 controls), Chile (680 cases, 442 controls), Denmark (366 cases, 766 controls), India (247 cases, 224 controls), and China (280 cases, 244 controls). Analysis of allelic imbalance in complementary DNA (cDNA) samples from human liver (n = 22) was performed using pyrosequencing. Transiently transfected HEK293 cells were used for [(3) H]-cholesterol export assays, analysis of protein expression, and localization of allelic constructs. Through fine mapping in German and Chilean samples, an ∼250 kB disease-associated interval could be defined for this locus. Lack of allelic imbalance or allelic splicing of the ABCG5 and ABCG8 transcripts in human liver limited the search to coding single nucleotide polymorphisms. Subsequent mutation detection and genotyping yielded two disease-associated variants: ABCG5-R50C (P = 4.94 × 10(-9) ) and ABCG8-D19H (P = 1.74 × 10(-10) ) in high pairwise linkage disequilibrium (r(2) = 0.95). [(3) H]-cholesterol export assays of allelic constructs harboring these genetic candidate variants demonstrated increased transport activity (3.2-fold, P = 0.003) only for the ABCG8-19H variant, which was also superior in nested logistic regression models in German (P = 0.018), Chilean (P = 0.030), and Chinese (P = 0.040) patient samples.

Conclusion: This variant thus provides a molecular basis for biliary cholesterol hypersecretion as the mechanism for cholesterol gallstone formation, thereby drawing a link between "postgenomic" and "pregenomic" pathophysiological knowledge about this common complex disorder. (HEPATOLOGY 2012).
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http://dx.doi.org/10.1002/hep.26009DOI Listing
June 2013

Significant role of estrogen and progesterone receptor sequence variants in gallbladder cancer predisposition: a multi-analytical strategy.

PLoS One 2012 10;7(7):e40162. Epub 2012 Jul 10.

Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India.

Background: Carcinoma of gallbladder (GBC) is an aggressive malignancy. The higher incidence of gallbladder cancer in women has been partly attributed to hormonal factors. Therefore the present study was designed to explore the role of genetic variants in estrogen (ESR1, ESR2) and progesterone (PGR) receptors in conferring risk of gallbladder cancer.

Materials And Methods: The present case-control study recruited total of 860 subjects, including 410 GBC patients, 230 gallstone patients and 220 controls. We examined the associations of 6 selected polymorphisms in three genes: ESR1 (rs2234693, rs9340799, rs1801132), ESR2 (rs1271572, rs1256049) and PGR (rs1042838) with GBC risk. Genotyping for all the polymorphisms was done using PCR-RFLP. Multifactor dimensionality reduction and classification and regression tree approaches were combined with logistic regression to discover high-order gene-gene interactions in hormonal pathway.

Results: On comparing the genotype frequency distribution in gallstone and GBC patients with that of healthy subjects, the homozygous variant genotypes of ESR1-397TT (rs2234693) polymorphism showed significant risk for developing gallstone [odds ratio: OR = 2.9] and GBC [OR = 1.8] respectively. Detailed haplotypes analysis suggested that ESR1 T( rs2234693)G( rs9340799)C( rs1801132) have significant association in conferring risk for both gallstones [OR = 2.2] and GBC [OR = 3.0]. However, the variant-containing genotypes (DI+II) of PGR (rs1042838) showed low risk in both GBC [OR = 0.4] and gallstone patients [OR = 0.4].On performing the MDR analysis, ESR1 IVS1-397C>T, ESR1 IVS1-351A>G, and ESR2-789 A>C yielded the highest testing accuracy of 0.634. These results were further supported by the CART analysis which revealed that individuals with the combined genotypes of ESR1-397 CT or TT, ESR1-351 AG or GG and ESR2 -789 AA had the highest risk for GBC [OR = 3.9].

Conclusion: Using multi-analytical approaches, our study showed important role of ESR1 IVS1-397C>T, ESR1 IVS1-351A>G, and ESR2-789 A>C variants in GBC susceptibility and the risk appears to be mediated through gallstone dependent pathway.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040162PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3393738PMC
March 2013

Association of matrix metalloproteinases (MMP2, MMP7 and MMP9) genetic variants with left ventricular dysfunction in coronary artery disease patients.

Clin Chim Acta 2012 Oct 1;413(19-20):1668-74. Epub 2012 Jun 1.

Department of Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences-SGPGIMS, Lucknow-226014 UP, India.

Background: Left ventricular dysfunction (LVD) is a condition resulting from clustered structural or functional cardiac disorder that reduces the ability of the ventricle to fill with or eject blood. The impaired ventricular function can be attributed to unfavorable ventricular remodeling. Among the pathways that contribute to remodeling process, matrix metalloproteinases (MMPs) appear to be of particular interest. We explored the association of MMP2 (C-735T, rs2285053), MMP7 (A-181G, rs11568818) and MMP9 (R279Q, rs17576), (P574R, rs2250889), (R668Q, rs17577) genetic variants with LVD in coronary artery disease (CAD) patients.

Methods: The study included 310 consecutive patients with angiographically confirmed CAD and 230 healthy controls. Among patients with CAD, 95 with reduced left ventricle ejection fraction (LVEF ≤ 45) were categorized as LVD. Polymorphisms were determined by PCR-RFLP.

Results: The MMP9 R668Q genetic variant was significantly associated with LVD (LVEF ≤ 45) (p value=0.009; OR=3.82). To validate our results, we performed a replication study in additional 200 cases with similar clinical characteristics and results again confirmed consistent findings (p value=0.033; OR=3.59). Also the frequency of haplotype R,P,Q comprising R668Q variation in MMP 9 was significantly higher in reduced LVEF subjects (p value=0.008; OR=1.83).

Conclusion: MMP9 R668Q plays important role in conferring susceptibility of LVD.
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http://dx.doi.org/10.1016/j.cca.2012.05.012DOI Listing
October 2012
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