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Current Protocols in Human Genetics

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https://www.readbyqxmd.com/read/29044473/induced-pluripotent-stem-cells-from-ovarian-tissue
#1
Sophia Salas, Nicholas Ng, Behzad Gerami-Naini, Raymond M Anchan
Yamanaka and colleagues revolutionized stem cell biology and regenerative medicine by observing that somatic cells can be reprogrammed into pluripotent stem cells. Evidence indicates that induced pluripotent stem (iPS) cells retain epigenetic memories that bias their spontaneous differentiation into the originating somatic cell type, therefore epigenetic memory may be exploited to improve tissue specific regeneration. We recently showed that iPS cells reprogrammed from ovarian granulosa cells using mouse and human tissue overwhelmingly differentiate homotypically into ovarian steroidogenic and primordial germ cells...
October 18, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29044472/population-stratification-in-genetic-association-studies
#2
Jacklyn N Hellwege, Jacob M Keaton, Ayush Giri, Xiaoyi Gao, Digna R Velez Edwards, Todd L Edwards
Population stratification (PS) is a primary consideration in studies of genetic determinants of human traits. Failure to control for PS may lead to confounding, causing a study to fail for lack of significant results, or resources to be wasted following false-positive signals. Here, historical and current approaches for addressing PS when performing genetic association studies in human populations are reviewed. Methods for detecting the presence of PS, including global and local ancestry methods, are described...
October 18, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29044471/analysis-and-annotation-of-whole-genome-or-whole-exome-sequencing-derived-variants-for-clinical-diagnosis
#3
Elizabeth A Worthey
Over the last 10 years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing or analysis (given access to appropriate tools), but rather clinical interpretation...
October 18, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29044470/analysis-of-gene-gene-interactions
#4
Brian S Cole, Molly A Hall, Ryan J Urbanowicz, Diane Gilbert-Diamond, Jason H Moore
The goal of this unit is to introduce epistasis, or gene-gene interactions, as a significant contributor to the genetic architecture of complex traits, including disease susceptibility. This unit begins with an historical overview of the concept of epistasis and the challenges inherent in the identification of potential gene-gene interactions. Then, it reviews statistical and machine learning methods for discovering epistasis in the context of genetic studies of quantitative and categorical traits. This unit concludes with a discussion of meta-analysis, replication, and other topics of active research...
October 18, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29044469/co-differentiation-of-human-pluripotent-stem-cells-derived-cardiomyocytes-and-endothelial-cells-from-cardiac-mesoderm-provides-a-three-dimensional-model-of-cardiac-microtissue
#5
Elisa Giacomelli, Milena Bellin, Valeria V Orlova, Christine L Mummery
The formation of cardiac mesodermal subtypes is highly regulated in time and space during heart development. In vitro models based on human pluripotent stem cells (hPS cells) provide opportunities to study mechanisms underlying fate choices governing lineage specification from common cardiovascular progenitors in human embryos. The generation of cardiac endothelial cells in particular allows the creation of complex models of cardiovascular disorders in which either cardiomyocytes or endothelial cells are affected...
October 18, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29044468/matchmaker-exchange
#6
Nara L M Sobreira, Harindra Arachchi, Orion J Buske, Jessica X Chong, Ben Hutton, Julia Foreman, François Schiettecatte, Tudor Groza, Julius O B Jacobsen, Melissa A Haendel, Kym M Boycott, Ada Hamosh, Heidi L Rehm
In well over half of the individuals with rare disease who undergo clinical or research next-generation sequencing, the responsible gene cannot be determined. Some reasons for this relatively low yield include unappreciated phenotypic heterogeneity; locus heterogeneity; somatic and germline mosaicism; variants of uncertain functional significance; technically inaccessible areas of the genome; incorrect mode of inheritance investigated; and inadequate communication between clinicians and basic scientists with knowledge of particular genes, proteins, or biological systems...
October 18, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28696560/overview-of-admixture-mapping
#7
Daniel Shriner
Admixture mapping is a powerful method of gene mapping for diseases or traits that show differential risk by ancestry. Admixture mapping has been applied most often to Americans who trace ancestry to various combinations of Native Americans, Europeans, and West Africans. Recent developments in admixture mapping include improvements in methods and the reference data needed to make inferences about ancestry, as well as extensions of the mapping approach in the framework of linear mixed models. In this unit, the key concepts of admixture mapping are outlined...
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28696559/genetic-testing-for-hereditary-nonpolyposis-colorectal-cancer-hnpcc
#8
Babi Ramesh Reddy Nallamilli, Madhuri Hegde
Hereditary nonpolyposis colorectal cancer (HNPCC), also called Lynch syndrome, is an autosomal dominant cancer syndrome that confers an elevated risk of early-onset colorectal cancer (CRC) and increased lifetime risk for other cancers of the endometrium, stomach, small intestine, hepatobiliary system, kidney, ureter, and ovary. Lynch syndrome accounts for up to 3% of all CRC, making it the most common hereditary colorectal cancer syndrome. Germline mutations in methyl-directed mismatch repair (MMR) genes give rise to microsatellite instability (MSI) in tumor DNA...
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28696558/mammalian-cell-tissue-culture
#9
Katy Phelan, Kristin M May
Cultured mammalian cells are used extensively in the field of human genetics. It requires a number of special skills in order to be able to preserve the structure, function, behavior, and biology of the cells in culture. This unit describes the basic skills required to maintain and preserve cell cultures: maintaining aseptic technique, preparing media with the appropriate characteristics, passaging, freezing and storage, recovering frozen stocks, and counting viable cells. © 2017 by John Wiley & Sons, Inc.
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28696557/microscopy-and-image-analysis
#10
George McNamara, Michael Difilippantonio, Thomas Ried, Frederick R Bieber
This unit provides an overview of light microscopy, including objectives, light sources, filters, film, and color photography for fluorescence microscopy and fluorescence in situ hybridization (FISH). We believe there are excellent opportunities for cytogeneticists, pathologists, and other biomedical readers, to take advantage of specimen optical clearing techniques and expansion microscopy-we briefly point to these new opportunities. © 2017 by John Wiley & Sons, Inc.
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28696556/1d-genome-sequencing-on-the-oxford-nanopore-minion
#11
Sara Goodwin, Robert Wappel, W Richard McCombie
Today's short-read sequencing instruments can generate read lengths between 50 bp and 700 bp depending on the specific instrument. These high-throughput sequencing approaches have revolutionized genomic science, allowing hundreds of thousands of full genomes to be sequenced, and have become indispensable tools for many researchers. With greater insight has come the revelation that many genomes are much more complicated than originally thought and include many rearrangements and copy-number variations. Unfortunately, short-read sequencing technologies are not well suited for identifying many of these types of events...
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28696555/copy-number-variants-detection-by-low-pass-whole-genome-sequencing
#12
Zirui Dong, Weiwei Xie, Haixiao Chen, Jinjin Xu, Huilin Wang, Yun Li, Jun Wang, Fang Chen, Kwong Wai Choy, Hui Jiang
Emerging studies have demonstrated that whole-genome sequencing (WGS) is an efficient tool for copy-number variants (CNV) detection, particularly in probe-poor regions, as compared to chromosomal microarray analysis (CMA). However, the cost of testing is beyond economical for routine usage and the lengthy turn-around time is not ideal for clinical implementation. In addition, the demand for computational resources also reduces the probability of clinical integration into each laboratory. Herein, a protocol providing CNV detection from low-pass, whole-genome sequencing (0...
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28384401/computational-approach-to-measuring-myocyte-disarray-in-animal-models-of-heart-disease
#13
William Wan, Leslie Leinwand
In cardiovascular disease research, studies often include measuring cardiac function and performing histological examination of heart tissue. After measuring contractility, hearts from animals such as mice and rats are often frozen or fixed, sliced, and stained to quantify the morphology of various structures such as extracellular matrix proteins, cell nuclei, and F-actin. Traditional scoring methods have largely consisted of assessing sections of images for the presence or absence of myocyte disarray. These approaches require unbiased manual assessment, which can require extra personnel, and are not scalable to the quantity of data that can be generated by modern automated experimental techniques...
April 6, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28384400/overview-of-genetic-diagnosis-in-cancer
#14
Bruce R Korf, Fady M Mikhail
Both cytogenetic and molecular genetic studies can contribute to the management of patients with cancer. In some cases, genetic markers are specific to particular tumor types and are useful in diagnosis. This can be helpful in distinguishing histologically similar tumors that may respond differently to treatment and can sometimes be of prognostic value. Genetic markers can also be tools for following the response of a tumor to therapy, providing a sensitive means to detect relapse. This introductory unit considers some of the types of genetic changes that occur in association with malignancies, as well as major approaches used in their detection...
April 6, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28384399/molecular-analysis-of-genetic-markers-for-non-hodgkin-lymphomas
#15
Lynette M Sholl, Janina Longtine, Frank C Kuo
Molecular analysis complements the clinical and histopathologic tools used to diagnose and subclassify hematologic malignancies. The presence of clonal antigen-receptor gene rearrangements can help to confirm the diagnosis of a B or T cell lymphoma and can serve as a fingerprint of that neoplasm to be used in identifying concurrent disease at disparate sites or recurrence at future time points. Certain lymphoid malignancies harbor a characteristic chromosomal translocation, a finding that may have significant implications for an individual's prognosis or response to therapy...
April 6, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28384398/methods-for-quantitative-creatinine-determination
#16
John F Moore, J Daniel Sharer
Reliable measurement of creatinine is necessary to assess kidney function, and also to quantitate drug levels and diagnostic compounds in urine samples. The most commonly used methods are based on the Jaffe principal of alkaline creatinine-picric acid complex color formation. However, other compounds commonly found in serum and urine may interfere with Jaffe creatinine measurements. Therefore, many laboratories have made modifications to the basic method to remove or account for these interfering substances...
April 6, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28384397/high-risk-screening-for-fabry-disease-analysis-by-tandem-mass-spectrometry-of-globotriaosylceramide-gb3-in-urine-collected-on-filter-paper
#17
Christiane Auray-Blais, Pamela Lavoie, Michel Boutin, Mona Abaoui
Fabry disease is a complex, panethnic lysosomal storage disorder. It is characterized by the accumulation of glycosphingolipids in tissues, organs, the vascular endothelium, and biological fluids. The reported incidence in different populations is quite variable, ranging from 1:1400 to 1:117,000. Its complexity lies in the marked genotypic and phenotypic heterogeneity. Despite the fact that it is an X-linked disease, more than 600 mutations affect both males and females. In fact, some females may be affected as severely as males...
April 6, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28075488/generating-exome-enriched-sequencing-libraries-from-formalin-fixed-paraffin-embedded-tissue-dna-for-next-generation-sequencing
#18
Beth A Marosy, Brian D Craig, Kurt N Hetrick, P Dane Witmer, Hua Ling, Sean M Griffith, Benjamin Myers, Elaine A Ostrander, Janet L Stanford, Lawrence C Brody, Kimberly F Doheny
This unit describes a technique for generating exome-enriched sequencing libraries using DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples. Utilizing commercially available kits, we present a low-input FFPE workflow starting with 50 ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in-solution-targeted selection for exons, followed by sequencing using the Illumina next-generation short-read sequencing platform...
January 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28075487/molecular-analysis-of-gene-rearrangements-and-mutations-in-acute-leukemias-and-myeloid-neoplasms
#19
Lynette M Sholl, Janina Longtine, Frank C Kuo
A subset of acute leukemias and other myeloid neoplasms contains specific genetic alterations, many of which are associated with unique clinical and pathologic features. These alterations include chromosomal rearrangements leading to oncogenic fusion proteins or alteration of gene expression by juxtaposing oncogenes to enhancer elements, as well as mutations leading to aberrant activation of a variety of proteins critical to hematopoietic progenitor cell proliferation and differentiation. Molecular analysis is central to diagnosis and clinical management of leukemias, permitting genetic confirmation of a clinical and histologic impression, providing prognostic and predictive information, and facilitating detection of minimal residual disease...
January 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28075486/highly-expandable-human-ips-cell-derived-neural-progenitor-cells-npc-and-neurons-for-central-nervous-system-disease-modeling-and-high-throughput-screening
#20
Chialin Cheng, Daniel M Fass, Kat Folz-Donahue, Marcy E MacDonald, Stephen J Haggarty
Reprogramming of human somatic cells into induced pluripotent stem (iPS) cells has greatly expanded the set of research tools available to investigate the molecular and cellular mechanisms underlying central nervous system (CNS) disorders. Realizing the promise of iPS cell technology for the identification of novel therapeutic targets and for high-throughput drug screening requires implementation of methods for the large-scale production of defined CNS cell types. Here we describe a protocol for generating stable, highly expandable, iPS cell-derived CNS neural progenitor cells (NPC) using multi-dimensional fluorescence activated cell sorting (FACS) to purify NPC defined by cell surface markers...
January 11, 2017: Current Protocols in Human Genetics
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