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Current Protocols in Human Genetics

Jessica N Cooke Bailey, Robert P Igo
The generation of genome-wide variation data has become commonplace. However, the potential for interpretation and application of these data for clinical assessment of outcomes of interest, and prediction of disease risk, is currently not fully realized. Many common, complex diseases now have numerous, well-established "risk" loci, and likely harbor many genetic determinants with effects too small to be detected at genome-wide levels of statistical significance. A simple and intuitive approach for converting genetic data to a predictive measure of disease susceptibility is to aggregate the risk effects of these loci into a single genetic risk score...
October 11, 2016: Current Protocols in Human Genetics
Jacob B Hall, William S Bush
Most analyses of genome-wide association data consider each variant independently without considering or adjusting for the genetic background present in the rest of the genome. New approaches to genome analysis use representations of genomic sharing to better account for confounding factors like population stratification or to directly approximate heritability through the estimated sharing of individuals in a dataset. These approaches use mixed linear models, which relate genotypic sharing to phenotypic sharing, and rely on the efficient computation of genetic sharing among individuals in a dataset...
October 11, 2016: Current Protocols in Human Genetics
S A Forbes, D Beare, N Bindal, S Bamford, S Ward, C G Cole, M Jia, C Kok, H Boutselakis, T De, Z Sondka, L Ponting, R Stefancsik, B Harsha, J Tate, E Dawson, S Thompson, H Jubb, P J Campbell
COSMIC ( is an expert-curated database of somatic mutations in human cancer. Broad and comprehensive in scope, recent releases in 2016 describe over 4 million coding mutations across all human cancer disease types. Mutations are annotated across the entire genome, but expert curation is focused on over 400 key cancer genes. Now encompassing the majority of molecular mutation mechanisms in oncogenetics, COSMIC additionally describes 10 million non-coding mutations, 1 million copy-number aberrations, 9 million gene-expression variants, and almost 8 million differentially methylated CpGs...
October 11, 2016: Current Protocols in Human Genetics
Sujata Chakraborty, Matteo Vatta, Linda L Bachinski, Ralf Krahe, Stephen Dlouhy, Shaochun Bai
Myotonic dystrophy types 1 (DM1) and 2 (DM2) are autosomal dominant, microsatellite repeat expansion disorders that affect muscle function. Myotonic dystrophy type 1 is caused by CTG repeat expansion in the 3' UTR region of the DMPK gene. Patients with DM2 have expansion of CCTG repeats in intron 1 of the CNBP gene. In this unit, we review and discuss the clinical phenotypes, genetic mutations causing the diseases, and the molecular diagnostic approaches and tools that are used to determine repeat sizes in DM1/2...
October 11, 2016: Current Protocols in Human Genetics
Judith A Hobert, Aiping Liu, Marzia Pasquali
Quantitative analysis of urine acylglycines has shown to be a highly sensitive and specific method with proven clinical utility for the diagnosis of several inherited metabolic disorders including: medium chain acyl-CoA dehydrogenase deficiency, multiple acyl-CoA dehydrogenase deficiency, short chain acyl-CoA dehydrogenase deficiency, 3-methylcrotonyl-CoA carboxylase deficiency, 2-methylbutyryl-CoA dehydrogenase deficiency, isovaleric acidemia, propionic academia, and isobutyryl-CoA dehydrogenase deficiency...
October 11, 2016: Current Protocols in Human Genetics
Samantha L P Schilit, Masato Ohtsuka, Rolen M Quadros, Channabasavaiah B Gurumurthy
Microinjection of DNA expression cassettes into fertilized zygotes has been a standard method for generating transgenic animal models. While efficient, the injected DNA integrates randomly into the genome, leading to potential disruption of endogenous genes or regulatory elements, variation in copy number, or integration into heterochromatic regions that inhibit transgene expression. A recently developed method addresses such pitfalls of traditional transgenesis by targeting the transgene to predetermined sites in the genome that can safely harbor exogenous DNA...
October 11, 2016: Current Protocols in Human Genetics
Mona Abaoui, Michel Boutin, Pamela Lavoie, Christiane Auray-Blais
Fabry disease is a multisystemic, X-linked lysosomal storage disorder caused by mutations in the GLA gene, leading to α-galactosidase A deficiency and resulting in the accumulation of glycosphingolipids in different tissues and biological fluids. Glycosphingolipid biomarkers, such as globotriaosylceramide (Gb3 ) isoforms, globotriaosylsphingosine (lyso-Gb3 ) and related analogs, and galabiosylceramide (Ga2 ) isoforms and analogs, are found to be abnormally increased in urine and in plasma of Fabry patients and have the potential to be used as specific biomarkers of the disease...
October 11, 2016: Current Protocols in Human Genetics
Robert P Igo, Jessica N Cooke Bailey, Jane Romm, Jonathan L Haines, Janey L Wiggs
The Illumina HumanExome BeadChip and other exome-based genotyping arrays offer inexpensive genotyping of some 240,000 mostly nonsynonymous coding variants across the human genome. The HumanExome chip, with its highly non-uniform distribution of markers and emphasis on rare coding variants, presents some unique challenges for quality control (QC) and data cleaning. Here, we describe QC procedures for HumanExome data, with examples of challenges specific to exome arrays from our experience cleaning a data set of ∼7,500 samples from the NEIGHBORHOOD Consortium...
July 1, 2016: Current Protocols in Human Genetics
Johan T den Dunnen
Consistent and unambiguous description of sequence variants is essential to report and exchange information on the analysis of a genome, in particular in DNA diagnostics. The HGVS nomenclature-recommendations for the description of sequence variants as originally proposed by the Human Genome Variation Society-has gradually been accepted as the international standard for variant description. In this unit, we describe the current recommendations (HGVS version 15.11) regarding how to describe variants at the DNA, RNA, and protein level...
2016: Current Protocols in Human Genetics
Liheng Wang, Dieter Egli, Rudolph L Leibel
The hypothalamus comprises neuronal clusters that are essential for body weight regulation and other physiological functions. Insights into the complex cellular physiology of this region of the brain are critical to understanding the pathogenesis of obesity, but human hypothalamic cells are largely inaccessible for direct study. Here we describe a technique for generation of arcuate-like hypothalamic neurons from human pluripotent stem (hPS) cells. Early activation of SHH signaling and inhibition of BMP and TGFβ signaling, followed by timed inhibition of NOTCH, can efficiently differentiate hPS cells into NKX2...
2016: Current Protocols in Human Genetics
Hans-Ulrich Klein, Martin Schäfer
The R package epigenomix has been designed to detect differentially transcribed gene isoforms that, in addition, exhibit altered histone modifications at their respective genomic loci. The package provides methods to map histone ChIP-seq profiles to isoforms and estimate their transcript abundances from RNA-seq data. Based on the differences observed between case and control samples in the RNA-seq and ChIP-seq data, a correlation measure is calculated for each isoform. The distribution of this correlation measure is further investigated by a Bayesian mixture model to (i) reveal the relationship between the studied histone modification and transcriptional activity, and (ii) detect specific isoforms with differences in both transcription values and histone modifications...
2016: Current Protocols in Human Genetics
Michel Boutin, Pamela Lavoie, Mona Abaoui, Christiane Auray-Blais
Fabry disease is an X-linked lysosomal storage disorder, caused by a deficit in α-galactosidase A enzyme activity, leading to the storage of sphingolipids such as globotriaosylsphingosine (lyso-Gb3 ), globotriaosylceramide (Gb3 ), and galabiosylceramide (Ga2 ) in organs, tissues and biological fluids. A recent metabolomic study performed in plasma revealed lyso-Gb3 analogs as novel Fabry disease biomarkers. These molecules correspond to lyso-Gb3 with different chemical modifications on the sphingosine chain (-C2 H4 , -H2 , +O, +H2 O, +H2 O2, and +H2 O3 )...
2016: Current Protocols in Human Genetics
Pamela Lavoie, Michel Boutin, Mona Abaoui, Christiane Auray-Blais
Fabry disease is an X-linked lysosomal storage disorder caused by the absence or reduction of the enzyme α-galactosidase A activity. Currently, globotriaosylsphingosine (lyso-Gb3 ) and globotriaosylceramide (Gb3 ) are used as biomarkers to diagnose and monitor Fabry patients. However, recent metabolomic studies have shown that several glycosphingolipids are also elevated in biological fluids of affected patients and may be related to disease manifestations. This unit describes a multiplex methodology targeting the analysis of urinary lyso-Gb3 and seven structurally related analogs...
2016: Current Protocols in Human Genetics
Christopher S Rogers
Animal models are an important resource for studying human diseases. Genetically engineered mice are the most commonly used species and have made significant contributions to our understanding of basic biology, disease mechanisms, and drug development. However, they often fail to recreate important aspects of human diseases and thus can have limited utility as translational research tools. Developing disease models in species more similar to humans may provide a better setting in which to study disease pathogenesis and test new treatments...
2016: Current Protocols in Human Genetics
Anne B S Giersch, Frederick R Bieber, Adrian M Dubuc, Jonathan A Fletcher, Azra H Ligon, Heather Mason-Suares, Cynthia C Morton, Stanislawa Weremowicz, Sheng Xiao, Paola Dal Cin
This appendix, developed by the staff at the Center for Advanced Molecular Diagnostics in the Department of Pathology at the Brigham and Women's Hospital, includes a comprehensive list of current "macros" or standardized statements used to facilitate reporting of cytogenetic results. These are provided as a useful reference for other laboratories. The statements are organized under the general categories of constitutional or acquired abnormalities and subdivided into analysis type (GTG-banding, FISH, or chromosomal microarray)...
2016: Current Protocols in Human Genetics
Steven M Harrison, Erin R Riggs, Donna R Maglott, Jennifer M Lee, Danielle R Azzariti, Annie Niehaus, Erin M Ramos, Christa L Martin, Melissa J Landrum, Heidi L Rehm
ClinVar is a freely accessible, public archive of reports of the relationships among genomic variants and phenotypes. To facilitate evaluation of the clinical significance of each variant, ClinVar aggregates submissions of the same variant, displays supporting data from each submission, and determines if the submitted clinical interpretations are conflicting or concordant. The unit describes how to (1) identify sequence and structural variants of interest in ClinVar by multiple searching approaches, including Variation Viewer and (2) understand the display of submissions to ClinVar and the evidence supporting each interpretation...
2016: Current Protocols in Human Genetics
Patrick R Gonzales, Andrew J Carroll, Bruce R Korf
Chromosome analysis is one of the first approaches to genetic testing and remains a key component of genetic analysis of constitutional and somatic genetic disorders. Numerical or unbalanced structural chromosome abnormalities usually lead to multiple congenital anomalies. Sometimes these are compatible with live birth, usually resulting in severe cognitive and physical handicaps; other times they result in miscarriage or stillbirth. Chromosome rearrangements also occur as somatic changes in malignancies. Identification of constitutional chromosomal anomalies (anomalies present in most or all cells of the body and/or the germline) can provide important information for genetic counseling...
2016: Current Protocols in Human Genetics
Libin Yuan, J Daniel Sharer
Homocysteine is a nonessential, sulfur-containing amino acid involved in one-carbon (folate) metabolism. A number of inherited and acquired conditions cause increased accumulation of this metabolite in blood (homocysteinemia) and other biofluids. Homocysteinemia is a risk factor for cardiovascular disease, including recurrent thrombosis. Accurate measurement of total plasma homocysteine is an important element in the diagnostic evaluation of these disorders. While a number of different methods have been developed for this purpose, the focus of this unit will be on a specific technique utilizing liquid chromatography-tandem mass spectrometry, which provides several advantages in terms of speed, sensitivity, and specificity...
2016: Current Protocols in Human Genetics
J Daniel Sharer
Biochemical genetics focuses on the pathophysiology, diagnosis, and treatment of inherited metabolic disorders. While individually rare, the combined incidence of these diseases makes them a significant source of morbidity and mortality, particularly among infants and young children, and new conditions continue to be identified. Inherited metabolic disorders may present as an acute, life-threatening illness or with more chronic, progressive symptoms. Population-scale newborn screening allows for early detection and treatment for >40 different metabolic disorders...
2016: Current Protocols in Human Genetics
Jonathan L Haines
No abstract text is available yet for this article.
2016: Current Protocols in Human Genetics
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