Publications by authors named "Shannon Rego"

22 Publications

  • Page 1 of 1

New Cases that Expand the Genotypic and Phenotypic Spectrum of Congenital NAD Deficiency Disorder.

Hum Mutat 2021 May 3. Epub 2021 May 3.

Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW, 2010, Australia.

Nicotinamide adenine dinucleotide (NAD) is an essential cofactor involved in over 400 cellular reactions. During embryogenesis, mammals synthesize NAD de novo from dietary L-tryptophan via the kynurenine pathway. Biallelic, inactivating variants in three genes encoding enzymes of this biosynthesis pathway (KYNU, HAAO, and NADSYN1) disrupt NAD synthesis and have been identified in patients with multiple malformations of the heart, kidney, vertebrae, and limbs; these patients have Congenital NAD Deficiency Disorder. Here we have identified a further three families with biallelic variants in HAAO and four families with biallelic variants in KYNU. These patients present similarly with multiple malformations of the heart, kidney, vertebrae, and limbs, of variable severity. We show that each variant identified in these patients results in loss-of-function, revealed by significant reduction in NAD levels via yeast genetic complementation assays. For the first time missense mutations are identified as a cause of malformation and shown to disrupt enzyme function. These missense and frameshift variants cause moderate to severe NAD deficiency in yeast, analogous to insufficient synthesized NAD in patients. We hereby expand the genotypic and corresponding phenotypic spectrum of Congenital NAD Deficiency Disorder. This article is protected by copyright. All rights reserved.
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http://dx.doi.org/10.1002/humu.24211DOI Listing
May 2021

Genomic Sequencing Results Disclosure in Diverse and Medically Underserved Populations: Themes, Challenges, and Strategies from the CSER Consortium.

J Pers Med 2021 Mar 13;11(3). Epub 2021 Mar 13.

Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA.

Genomic sequencing results need to be effectively communicated across all populations and practice settings. Projects in the Clinical Sequencing Evidence-Generating Research (CSER) consortium enroll diverse racial/ethnic and medically underserved participants across various clinical contexts. This article explores a set of CSER results disclosure cases to expand the evidence base on experiences returning genomic results. Case details were collected using a structured set of questions. We identified common themes in the case set, and assessed challenges and strategies in achieving six relevant results disclosure objectives. CSER-affiliated patient/community stakeholder impressions of the findings were solicited via video conference calls. Seventeen cases across six CSER projects were included. Case themes sorted into four categories: (1) factors influencing participant understanding, (2) participant emotional response, (3) disease burden, and (4) logistical challenges. Challenges meeting results disclosure objectives included a lack of dialogue, health literacy level, unexpected findings, and complex concepts. Strategies were consistent with traditional genetic counseling practice, but also highlighted approaches being evaluated in CSER projects. Patient/community stakeholders supported the identified themes and provided additional suggestions to improve patient understanding and engagement. These experiences add valuable insights into adapting genomic results disclosure practices to best serve all patient populations.
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http://dx.doi.org/10.3390/jpm11030202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7998798PMC
March 2021

A review and definition of 'usual care' in genetic counseling trials to standardize use in research.

J Genet Couns 2021 Feb 5;30(1):42-50. Epub 2020 Dec 5.

Department of Humanities and Social Sciences, University of California, San Francisco, CA, USA.

The descriptor 'usual care' refers to standard or routine care. Yet, no formal definition exists. The need to define what constitutes usual care arises in clinical research. Often one arm in a trial represents usual care in comparison with a novel intervention. Accordingly, usual care in genetic counseling research appears predominantly in randomized controlled trials. Recent standards for reporting genetic counseling research call for standardization, but do not address usual care. We (1) inventoried all seven studies in the Clinical Sequencing Evidence-Generating Consortium (CSER) about how genetic counseling was conceptualized, conducted, and whether a usual care arm was involved; (2) conducted a review of published randomized control trials in genetic counseling, comparing how researchers describe usual care groups; and (3) reviewed existing professionally endorsed definitions and practice descriptions of genetic counseling. We found wide variation in the content and delivery of usual care. Descriptions frequently detailed the content of usual care, most often noting assessment of genetic risk factors, collecting family histories, and offering testing. A minority included addressing psychological concerns or the risks versus benefits of testing. Descriptions of how care was delivered were vague except for mode and type of clinician, which varied. This significant variation, beyond differences expected among subspecialties, reduces the validity and generalizability of genetic counseling research. Ideally, research reflects clinical practice so that evidence generated can be used to improve clinical outcomes. To address this objective, we propose a definition of usual care in genetic counseling research that merges common elements from the National Society of Genetic Counselors' practice definition, the Reciprocal Engagement Model, and the Accreditation Council for Genetic Counselors' practice-based competencies. Promoting consistent execution of usual care in the design of genetic counseling trials can lead to more consistency in representing clinical care and facilitate the generation of evidence to improve it.
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http://dx.doi.org/10.1002/jgc4.1363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7882019PMC
February 2021

Candidate variants in TUB are associated with familial tremor.

PLoS Genet 2020 09 21;16(9):e1009010. Epub 2020 Sep 21.

Department of Genetics, Stanford University, Stanford, CA, United States of America.

Essential tremor (ET) is the most common adult-onset movement disorder. In the present study, we performed whole exome sequencing of a large ET-affected family (10 affected and 6 un-affected family members) and identified a TUB p.V431I variant (rs75594955) segregating in a manner consistent with autosomal-dominant inheritance. Subsequent targeted re-sequencing of TUB in 820 unrelated individuals with sporadic ET and 630 controls revealed significant enrichment of rare nonsynonymous TUB variants (e.g. rs75594955: p.V431I, rs1241709665: p.Ile20Phe, rs55648406: p.Arg49Gln) in the ET cohort (SKAT-O test p-value = 6.20e-08). TUB encodes a transcription factor predominantly expressed in neuronal cells and has been previously implicated in obesity. ChIP-seq analyses of the TUB transcription factor across different regions of the mouse brain revealed that TUB regulates the pathways responsible for neurotransmitter production as well thyroid hormone signaling. Together, these results support the association of rare variants in TUB with ET.
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http://dx.doi.org/10.1371/journal.pgen.1009010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7529431PMC
September 2020

iPSC Modeling of RBM20-Deficient DCM Identifies Upregulation of RBM20 as a Therapeutic Strategy.

Cell Rep 2020 09;32(10):108117

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany; Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA, USA; Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA; DZHK: German Center for Cardiovascular Research, Partner Site EMBL Heidelberg, Heidelberg, Germany. Electronic address:

Recent advances in induced pluripotent stem cell (iPSC) technology and directed differentiation of iPSCs into cardiomyocytes (iPSC-CMs) make it possible to model genetic heart disease in vitro. We apply CRISPR/Cas9 genome editing technology to introduce three RBM20 mutations in iPSCs and differentiate them into iPSC-CMs to establish an in vitro model of RBM20 mutant dilated cardiomyopathy (DCM). In iPSC-CMs harboring a known causal RBM20 variant, the splicing of RBM20 target genes, calcium handling, and contractility are impaired consistent with the disease manifestation in patients. A variant (Pro633Leu) identified by exome sequencing of patient genomes displays the same disease phenotypes, thus establishing this variant as disease causing. We find that all-trans retinoic acid upregulates RBM20 expression and reverts the splicing, calcium handling, and contractility defects in iPSC-CMs with different causal RBM20 mutations. These results suggest that pharmacological upregulation of RBM20 expression is a promising therapeutic strategy for DCM patients with a heterozygous mutation in RBM20.
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http://dx.doi.org/10.1016/j.celrep.2020.108117DOI Listing
September 2020

The expanding spectrum of NFIB-associated phenotypes in a diverse patient population-A report of two new patients.

Am J Med Genet A 2020 12 9;182(12):2959-2963. Epub 2020 Sep 9.

Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA.

NFIB (Nuclear Factor I B) haploinsufficiency has recently been identified as a cause of intellectual disability and macrocephaly. Here we describe two patients with pathogenic variants in NFIB. The first is a 6-year-old Latino male with developmental delays, mild hypotonia, facial anomalies, and brain magnetic resonance imaging findings comprising mild thinning of the corpus callosum, with more marked thinning of the splenium and blunting of the rostrum and cavum septum pellucidum. Exome sequencing identified a previously described de novo variant in NFIB, c.265C>T, predicting p.Arg89Ter. The second is a 5-year-old Latino male with developmental delays, hypotonia, dysmorphic features, a preauricular tag and pit, a small ventricular septal defect, and brain magnetic resonance imaging findings including a dysmorphic corpus callosum and a small posterior fossa. A single nucleotide polymorphism microarray identified a 92 kb interstitial deletion at 9p23 including several exons of NFIB and no other known genes. Our two patients add to the knowledge of this rare condition through our addition of new brain MRI findings and dysmorphic features. Additionally, these are the first known Latino patients to be described with NFIB haploinsufficiency, expanding our understanding of the associated facial features in diverse populations. Further data are needed to determine genotype-phenotype relationships for NFIB.
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http://dx.doi.org/10.1002/ajmg.a.61852DOI Listing
December 2020

Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7.

Genet Med 2020 07 7;22(7):1215-1226. Epub 2020 May 7.

Department of Medical Genetics, Lyon Hospices Civils, Lyon, France.

Purpose: Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts.

Methods: We performed exome, targeted capture, and Sanger sequencing of patients with undiagnosed developmental disorders, in multiple independent diagnostic or research centers. Phenotypic and mutational comparisons were facilitated through data exchange platforms. Whole-transcriptome sequencing was performed on RNA from patient- and control-derived fibroblasts.

Results: We identified heterozygous missense variants in TRAF7 as the cause of a developmental delay-malformation syndrome in 45 patients. Major features include a recognizable facial gestalt (characterized in particular by blepharophimosis), short neck, pectus carinatum, digital deviations, and patent ductus arteriosus. Almost all variants occur in the WD40 repeats and most are recurrent. Several differentially expressed genes were identified in patient fibroblasts.

Conclusion: We provide the first large-scale analysis of the clinical and mutational spectrum associated with the TRAF7 developmental syndrome, and we shed light on its molecular etiology through transcriptome studies.
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http://dx.doi.org/10.1038/s41436-020-0792-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8093014PMC
July 2020

A novel truncating variant in ring finger protein 113A (RNF113A) confirms the association of this gene with X-linked trichothiodystrophy.

Am J Med Genet A 2020 03 27;182(3):513-520. Epub 2019 Dec 27.

Division of Medical Genetics, University of California, San Francisco, San Francisco, California.

We describe an 11-year old boy with severe global developmental delays, failure to thrive and growth retardation, refractory seizures with recurrent status epilepticus, hypogammaglobulinemia, hypergonadotropic hypogonadism, and duodenal strictures. He had facial and skin findings compatible with trichothiodystrophy, including sparse and brittle hair, thin eyebrows, and dry skin. Exome sequencing showed a hemizygous, truncating variant in RNF113A, c.903_910delGCAGACCA, predicting p.(Gln302fs*12), that was inherited from his mother. Although his clinical features overlap closely with features described in the two previously reported male first cousins with RNF113A loss of function mutations, the duodenal strictures seen in this patient have not been reported. Interestingly, the patient's mother had short stature and 100% skewed X-inactivation as seen in other obligate female carriers. A second male with developmental delays, microcephaly, seizures, ambiguous genitalia, and facial anomalies that included sparse and brittle hair, thin eyebrows and dry skin was recently reported to have c.897_898delTG, predicting p.(Cys299*) in RNF113A and we provide additional clinical details for this patient. This report further supports deleterious variants in RNF113A as a cause of a novel trichothiodystrophy syndrome.
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http://dx.doi.org/10.1002/ajmg.a.61450DOI Listing
March 2020

Informed Consent in the Genomics Era.

Cold Spring Harb Perspect Med 2020 08 3;10(8). Epub 2020 Aug 3.

Stanford Center for Biomedical Ethics, Stanford, California 94305, USA.

Informed consent, the process of gathering autonomous authorization for a medical intervention or medical research participation, is a fundamental component of medical practice. Medical informed consent assumes decision-making capacity, voluntariness, comprehension, and adequate information. The increasing use of genetic testing, particularly genomic sequencing, in clinical and research settings has presented many new challenges for clinicians and researchers when obtaining informed consent. Many of these challenges revolve around the need for patient comprehension of sufficient information. Genomic sequencing is complex-all of the possible results are too numerous to explain, and many of the risks and benefits remain unknown. Thus, historical standards of consent are difficult to apply. Alternative models of consent have been proposed to increase patient understanding, and several have empirically demonstrated effectiveness. However, there is still a striking lack of consensus in the genetics community about what constitutes informed consent in the context of genomic sequencing. Multiple approaches are needed to address this challenge, including consensus building around standards, targeted use of genetic counselors in nongenetics clinics in which genomic testing is ordered, and the development and testing of alternative models for obtaining informed consent.
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http://dx.doi.org/10.1101/cshperspect.a036582DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397836PMC
August 2020

Developmental and epileptic encephalopathy in two siblings with a novel, homozygous missense variant in SCN1B.

Am J Med Genet A 2019 11 29;179(11):2190-2195. Epub 2019 Aug 29.

Institute for Human Genetics, University of California San Francisco, San Francisco, California.

Developmental and epileptic encephalopathies are genetic disorders in which both the developmental disability and the frequent epileptic activity are the effect of a specific gene variant. While heterozygous variants in SCN1B have been described in families with generalized epilepsy with febrile seizures plus, Type 1, only three cases of homozygous, missense variants in SCN1B have been reported in association with autosomal recessive inheritance of a severe developmental and epileptic encephalopathy. We present two siblings who are homozygous for a novel, missense variant in SCN1B, c.265C>T, predicting p.Arg89Cys. The proband is an 11-year-old female with infantile-onset, fever-induced, intractable generalized tonic-clonic seizures, myoclonic seizures, and developmental slowing and autism spectrum disorder occurring later in the course of the disease. Her 4-year-old brother had a similar epilepsy phenotype, but still displays normal development. This variant has not been previously reported in the homozygous state in control databases. The variant was predicted to be damaging and occurred in the vicinity of other epileptic encephalopathy-associated missense variants that are biallelic and located in the extracellular immunoglobulin loop domain of the protein, which mediates interaction of the beta-1 subunit with cellular adhesion molecules. Our report is the first set of siblings with homozygosity for the p.Arg89Cys variant in SCN1B and further implicates biallelic mutations in this gene as a cause of epileptic encephalopathy mimicking Dravet syndrome. Interestingly, the phenotype we observed was milder compared to that previously described in patients with recessive SCN1B mutations.
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http://dx.doi.org/10.1002/ajmg.a.61344DOI Listing
November 2019

Longitudinal multi-omics of host-microbe dynamics in prediabetes.

Nature 2019 05 29;569(7758):663-671. Epub 2019 May 29.

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.

Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early disease stages, its effects on biological processes or the transition to clinical T2D. To understand the earliest stages of T2D better, we obtained samples from 106 healthy individuals and individuals with prediabetes over approximately four years and performed deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, as well as changes in the microbiome. This rich longitudinal data set revealed many insights: first, healthy profiles are distinct among individuals while displaying diverse patterns of intra- and/or inter-personal variability. Second, extensive host and microbial changes occur during respiratory viral infections and immunization, and immunization triggers potentially protective responses that are distinct from responses to respiratory viral infections. Moreover, during respiratory viral infections, insulin-resistant participants respond differently than insulin-sensitive participants. Third, global co-association analyses among the thousands of profiled molecules reveal specific host-microbe interactions that differ between insulin-resistant and insulin-sensitive individuals. Last, we identified early personal molecular signatures in one individual that preceded the onset of T2D, including the inflammation markers interleukin-1 receptor agonist (IL-1RA) and high-sensitivity C-reactive protein (CRP) paired with xenobiotic-induced immune signalling. Our study reveals insights into pathways and responses that differ between glucose-dysregulated and healthy individuals during health and disease and provides an open-access data resource to enable further research into healthy, prediabetic and T2D states.
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http://dx.doi.org/10.1038/s41586-019-1236-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6666404PMC
May 2019

A longitudinal big data approach for precision health.

Nat Med 2019 05 8;25(5):792-804. Epub 2019 May 8.

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.

Precision health relies on the ability to assess disease risk at an individual level, detect early preclinical conditions and initiate preventive strategies. Recent technological advances in omics and wearable monitoring enable deep molecular and physiological profiling and may provide important tools for precision health. We explored the ability of deep longitudinal profiling to make health-related discoveries, identify clinically relevant molecular pathways and affect behavior in a prospective longitudinal cohort (n = 109) enriched for risk of type 2 diabetes mellitus. The cohort underwent integrative personalized omics profiling from samples collected quarterly for up to 8 years (median, 2.8 years) using clinical measures and emerging technologies including genome, immunome, transcriptome, proteome, metabolome, microbiome and wearable monitoring. We discovered more than 67 clinically actionable health discoveries and identified multiple molecular pathways associated with metabolic, cardiovascular and oncologic pathophysiology. We developed prediction models for insulin resistance by using omics measurements, illustrating their potential to replace burdensome tests. Finally, study participation led the majority of participants to implement diet and exercise changes. Altogether, we conclude that deep longitudinal profiling can lead to actionable health discoveries and provide relevant information for precision health.
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http://dx.doi.org/10.1038/s41591-019-0414-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6713274PMC
May 2019

Much ado about nothing: A qualitative study of the experiences of an average-risk population receiving results of exome sequencing.

J Genet Couns 2019 04 5;28(2):428-437. Epub 2019 Mar 5.

Department of Genetics, Stanford University School of Medicine, Stanford, California.

The increasing availability of exome sequencing to the general ("healthy") population raises questions about the implications of genomic testing for individuals without suspected Mendelian diseases. Little is known about this population's motivations for undergoing exome sequencing, their expectations, reactions, and perceptions of utility. In order to address these questions, we conducted in-depth semi-structured interviews with 12 participants recruited from a longitudinal multi-omics profiling study that included exome sequencing. Participants were interviewed after receiving exome results, which included Mendelian disease-associated pathogenic and likely pathogenic variants, pharmacogenetic variants, and risk assessments for multifactorial diseases such as type 2 diabetes. The primary motivation driving participation in exome sequencing was personal curiosity. While they reported feeling validation and relief, participants were frequently underwhelmed by the results and described having expected more from exome sequencing. All participants reported discussing the results with at least some family, friends, and healthcare providers. Participants' recollection of the results returned to them was sometimes incorrect or incomplete, in many cases aligning with their perceptions of their health risks when entering the study. These results underscore the need for different genetic counseling approaches for generally healthy patients undergoing exome sequencing, in particular the need to provide anticipatory guidance to moderate participants' expectations. They also provide a preview of potential challenges clinicians may face as genomic sequencing continues to scale-up in the general population despite a lack of full understanding of its impact.
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http://dx.doi.org/10.1002/jgc4.1096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456364PMC
April 2019

Developing a genomics rotation: Practical training around variant interpretation for genetic counseling students.

J Genet Couns 2019 04 1;28(2):466-476. Epub 2019 Feb 1.

Department of Genetics, Stanford University School of Medicine, Stanford, California.

With the wide adoption of next-generation sequencing (NGS)-based genetic tests, genetic counselors require increased familiarity with NGS technology, variant interpretation concepts, and variant assessment tools. The use of exome and genome sequencing in clinical care has expanded the reach and diversity of genetic testing. Regardless of the setting where genetic counselors are performing variant interpretation or reporting, most of them have learned these skills from colleagues, while on the job. Though traditional, lecture-based learning around these topics is important, there has been growing need for the inclusion of case-based, experiential training of genomics and variant interpretation for genetic counseling students, with the goal of creating a strong foundation in variant interpretation for new genetic counselors, regardless of what area of practice they enter. To address this need, we established a genomics and variant interpretation rotation for Stanford's genetic counseling training program. In response to changes in the genomics landscape, this has now evolved into three unique rotation experiences, each focused on variant interpretation in the context of various genomic settings, including clinical laboratory, research laboratory, and healthy genomic analysis studies. Here, we describe the goals and learning objectives that we have developed for these variant interpretation rotations, and illustrate how these concepts are applied in practice.
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http://dx.doi.org/10.1002/jgc4.1094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456376PMC
April 2019

High-frequency actionable pathogenic exome variants in an average-risk cohort.

Cold Spring Harb Mol Case Stud 2018 12 17;4(6). Epub 2018 Dec 17.

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.

Exome sequencing is increasingly utilized in both clinical and nonclinical settings, but little is known about its utility in healthy individuals. Most previous studies on this topic have examined a small subset of genes known to be implicated in human disease and/or have used automated pipelines to assess pathogenicity of known variants. To determine the frequency of both medically actionable and nonactionable but medically relevant exome findings in the general population we assessed the exomes of 70 participants who have been extensively characterized over the past several years as part of a longitudinal integrated multiomics profiling study. We analyzed exomes by identifying rare likely pathogenic and pathogenic variants in genes associated with Mendelian disease in the Online Mendelian Inheritance in Man (OMIM) database. We then used American College of Medical Genetics (ACMG) guidelines for the classification of rare sequence variants. Additionally, we assessed pharmacogenetic variants. Twelve out of 70 (17%) participants had medically actionable findings in Mendelian disease genes. Five had phenotypes or family histories associated with their genetic variants. The frequency of actionable variants is higher than that reported in most previous studies and suggests added benefit from utilizing expanded gene lists and manual curation to assess actionable findings. A total of 63 participants (90%) had additional nonactionable findings, including 60 who were found to be carriers for recessive diseases and 21 who have increased Alzheimer's disease risk because of heterozygous or homozygous e4 alleles (18 participants had both). Our results suggest that exome sequencing may have considerably more utility for health management in the general population than previously thought.
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http://dx.doi.org/10.1101/mcs.a003178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318774PMC
December 2018

Evidence-based assessments of clinical actionability in the context of secondary findings: Updates from ClinGen's Actionability Working Group.

Hum Mutat 2018 11;39(11):1677-1685

Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon.

The use of genome-scale sequencing allows for identification of genetic findings beyond the original indication for testing (secondary findings). The ClinGen Actionability Working Group's (AWG) protocol for evidence synthesis and semi-quantitative metric scoring evaluates four domains of clinical actionability for potential secondary findings: severity and likelihood of the outcome, and effectiveness and nature of the intervention. As of February 2018, the AWG has scored 127 genes associated with 78 disorders (up-to-date topics/scores are available at www.clinicalgenome.org). Scores across these disorders were assessed to compare genes/disorders recommended for return as secondary findings by the American College of Medical Genetics and Genomics (ACMG) with those not currently recommended. Disorders recommended by the ACMG scored higher on outcome-related domains (severity and likelihood), but not on intervention-related domains (effectiveness and nature of the intervention). Current practices indicate that return of secondary findings will expand beyond those currently recommended by the ACMG. The ClinGen AWG evidence reports and summary scores are not intended as classifications of actionability, rather they provide a resource to aid decision makers as they determine best practices regarding secondary findings. The ClinGen AWG is working with the ACMG Secondary Findings Committee to update future iterations of their secondary findings list.
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http://dx.doi.org/10.1002/humu.23631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211797PMC
November 2018

High Throughput Sequencing and Assessing Disease Risk.

Cold Spring Harb Perspect Med 2019 01 2;9(1). Epub 2019 Jan 2.

Department of Genetics, Stanford University, Stanford, California 94305.

High-throughput sequencing has dramatically improved our ability to determine and diagnose the underlying causes of human disease. The use of whole-genome and whole-exome sequencing has facilitated faster and more cost-effective identification of new genes implicated in Mendelian disease. It has also improved our ability to identify disease-causing mutations for Mendelian diseases whose associated genes are already known. These benefits apply not only in cases in which the objective is to assess genetic disease risk in adults and children, but also for prenatal genetic testing and embryonic testing. High-throughput sequencing has also impacted our ability to assess risk for complex diseases and will likely continue to influence this area of disease research as more and more individuals undergo sequencing and we better understand the significance of variation, both rare and common, across the genome. Through these activities, high-throughput sequencing has the potential to revolutionize medicine.
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http://dx.doi.org/10.1101/cshperspect.a026849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6314070PMC
January 2019

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.

Cell Syst 2018 Feb 17;6(2):157-170.e8. Epub 2018 Jan 17.

Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Canary Center at Stanford, Stanford University School of Medicine, Stanford, CA 94305, USA.

Advances in omics technologies now allow an unprecedented level of phenotyping for human diseases, including obesity, in which individual responses to excess weight are heterogeneous and unpredictable. To aid the development of better understanding of these phenotypes, we performed a controlled longitudinal weight perturbation study combining multiple omics strategies (genomics, transcriptomics, multiple proteomics assays, metabolomics, and microbiomics) during periods of weight gain and loss in humans. Results demonstrated that: (1) weight gain is associated with the activation of strong inflammatory and hypertrophic cardiomyopathy signatures in blood; (2) although weight loss reverses some changes, a number of signatures persist, indicative of long-term physiologic changes; (3) we observed omics signatures associated with insulin resistance that may serve as novel diagnostics; (4) specific biomolecules were highly individualized and stable in response to perturbations, potentially representing stable personalized markers. Most data are available open access and serve as a valuable resource for the community.
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http://dx.doi.org/10.1016/j.cels.2017.12.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6021558PMC
February 2018

A Case Report of Hypoglycemia and Hypogammaglobulinemia: DAVID Syndrome in a Patient With a Novel NFKB2 Mutation.

J Clin Endocrinol Metab 2017 07;102(7):2127-2130

Division of Allergy, Immunology & Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305.

Context: Deficient anterior pituitary with variable immune deficiency (DAVID) syndrome is a rare disorder in which children present with symptomatic adrenocorticotropic hormone (ACTH) deficiency preceded by hypogammaglobulinemia from B-cell dysfunction with recurrent infections, called common variable immunodeficiency (CVID). Subsequent whole exome sequencing studies have revealed germline heterozygous C-terminal mutations of NFKB2 as a cause of DAVID syndrome or of CVID without clinical hypopituitarism. However, to the best of our knowledge there have been no cases in which the endocrinopathy has presented in the absence of a prior clinical history of CVID.

Case Description: A previously healthy 7-year-old boy with no history of clinical immunodeficiency presented with profound hypoglycemia and seizures. He was found to have secondary adrenal insufficiency and was started on glucocorticoid replacement. An evaluation for autoimmune disease, including for antipituitary antibodies, was negative. Evaluation unexpectedly revealed hypogammaglobulinemia [decreased immunoglobulin G (IgG), IgM, and IgA]. He had moderately reduced serotype-specific IgG responses after pneumococcal polysaccharide vaccine. Subsequently, he was found to have growth hormone deficiency. Six years after initial presentation, whole exome sequencing revealed a de novo heterozygous NFKB2 missense mutation c.2596A>C (p.Ser866Arg) in the C-terminal region predicted to abrogate the processing of the p100 NFKB2 protein to its active p52 form.

Conclusions: Isolated early-onset ACTH deficiency is rare, and C-terminal region NFKB2 mutations should be considered as an etiology even in the absence of a clinical history of CVID. Early immunologic evaluation is indicated in the diagnosis and management of isolated ACTH deficiency.
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http://dx.doi.org/10.1210/jc.2017-00341DOI Listing
July 2017

Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information.

PLoS Biol 2017 01 12;15(1):e2001402. Epub 2017 Jan 12.

Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America.

A new wave of portable biosensors allows frequent measurement of health-related physiology. We investigated the use of these devices to monitor human physiological changes during various activities and their role in managing health and diagnosing and analyzing disease. By recording over 250,000 daily measurements for up to 43 individuals, we found personalized circadian differences in physiological parameters, replicating previous physiological findings. Interestingly, we found striking changes in particular environments, such as airline flights (decreased peripheral capillary oxygen saturation [SpO2] and increased radiation exposure). These events are associated with physiological macro-phenotypes such as fatigue, providing a strong association between reduced pressure/oxygen and fatigue on high-altitude flights. Importantly, we combined biosensor information with frequent medical measurements and made two important observations: First, wearable devices were useful in identification of early signs of Lyme disease and inflammatory responses; we used this information to develop a personalized, activity-based normalization framework to identify abnormal physiological signals from longitudinal data for facile disease detection. Second, wearables distinguish physiological differences between insulin-sensitive and -resistant individuals. Overall, these results indicate that portable biosensors provide useful information for monitoring personal activities and physiology and are likely to play an important role in managing health and enabling affordable health care access to groups traditionally limited by socioeconomic class or remote geography.
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http://dx.doi.org/10.1371/journal.pbio.2001402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5230763PMC
January 2017

Association of AHSG with alopecia and mental retardation (APMR) syndrome.

Hum Genet 2017 03 4;136(3):287-296. Epub 2017 Jan 4.

Department of Genetics, Stanford University, Stanford, CA, USA.

Alopecia with mental retardation syndrome (APMR) is a very rare autosomal recessive condition that is associated with total or partial absence of hair from the scalp and other parts of the body as well as variable intellectual disability. Here we present whole-exome sequencing results of a large consanguineous family segregating APMR syndrome with seven affected family members. Our study revealed a novel predicted pathogenic, homozygous missense mutation in the AHSG (OMIM 138680) gene (AHSG: NM_001622:exon7:c.950G>A:p.Arg317His). The variant is predicted to affect a region of the protein required for protein processing and disrupts a phosphorylation motif. In addition, the altered protein migrates with an aberrant size relative to healthy individuals. Consistent with the phenotype, AHSG maps within APMR linkage region 1 (APMR 1) as reported before, and falls within runs of homozygosity (ROH). Previous families with APMR syndrome have been studied through linkage analyses and the linkage resolution did not allow pointing out to a single gene candidate. Our study is the first report to identify a homozygous missense mutation for APMR syndrome through whole-exome sequencing.
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http://dx.doi.org/10.1007/s00439-016-1756-5DOI Listing
March 2017

Newborn screening in the genomics era.

Authors:
Shannon Rego

J Law Biosci 2014 Sep 16;1(3):369-377. Epub 2014 Oct 16.

Stanford University, CA 94305, USA.

Newborn screening (NBS) exists in every state for the purpose of testing newborns for genetic medical conditions that can be severe, may be treatable, and are often not clinically evident at birth. While almost all of the diseases screened for in newborns have underlying genetic causes, NBS in its current form is performed not by testing for genetic mutations, but by testing for biochemical markers that indicate a disorder. The potential use of whole-genome newborn screening (WG-NBS) as an alternative to the current biochemical testing utilized for NBS would dramatically expand the quantity and types of information parents could learn from screening and is likely to have many implications, both positive and negative. As whole-genome sequencing (WGS) becomes more economical, it probably will be used for the purposes of NBS. However, such an expansion of NBS would contradict many of the principles that have historically guided public health screening programs and, if implemented without sufficient preparation, could result in insufficient infrastructure to accommodate the health care and data management needs that would arise. This article will first look at the past and present of NBS, then the rise of whole genome sequencing, before considering the challenges of WG-NBS, and will end with some thoughts on the path forward.
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http://dx.doi.org/10.1093/jlb/lsu027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5033535PMC
September 2014