An efficient SNP system for mouse genome scanning and elucidating strain relationships

A set of 1638 informative SNP markers easily assayed by the Amplifluor genotyping system were tested in 102 mouse strains, including the majority of the common and wild-derived inbred strains available from The Jackson Laboratory. Selected from publicly available databases, the markers are on average ~1.5 Mb apart and, whenever possible, represent the rare allele in at least two strains. Amplifluor assays were developed for each marker and performed on two independent DNA samples from each strain. The mean number of polymorphisms between strains was 608±136 SD. Several tests indicate that the markers provide an effective system for performing genome scans and quantitative trait loci analyses in all but the most closely related strains. Additionally, the markers revealed several subtle differences between closely related mouse strains, including the groups of several 129, BALB, C3H, C57, and DBA strains, and a group of wild-derived inbred strains representing several Mus musculus subspecies. Applying a neighbor-joining method to the data, we constructed a mouse strain family tree, which in most cases confirmed existing genealogies.     

Power and SNP tagging in whole mitochondrial genome association studies

The application of genetic association studies to detect mitochondrial variants responsible for phenotypic variation has recently been demonstrated. However, the only power estimates currently available are based on the use of mitochondrial haplogroups, which can only tag a small fraction of the common variation in the mitochondrial genome. Here, power estimates are derived for a SNP-based study design for both disease (case-control) and quantitative trait mapping studies. Power is estimated using simulations based on a collection of publicly available mitochondrial sequences of European origin. The power when testing all common mitochondrial SNPs is shown to be equivalent to that when testing only tagging SNPs, despite the relatively high ratio of tagging SNPs to total SNPs resulting from the tagging of all SNPs with a minor allele frequency greater than 1%. The sample size requirements of mitochondrial genome association studies are compared with that of nuclear whole-genome studies. Remarkably, the trade off between the number of tests being performed and the proportion of phenotypic variance explained for a fixed effect size results in approximately equal sample sizes required for both study types, although the per individual cost for the mitochondrial association study is much less. To test the representation of the sequences used in the power simulations, a sample of 3839 individuals from 1037 Australian families was genotyped for 69 tagging SNPs. The strong concordance in allele frequencies and linkage disequilibrium between the European sequences and the Australian sample indicates that the results presented here are transferable across populations of European descent.     

应用全基因组扩增技术对β-地中海贫血进行胚胎植入前遗传学诊断

目的 探讨对β-地中海贫血进行胚胎植入前遗传学诊断的方法。方法 夫妇双方分别为β41-42(-TCTT)及IVS-I 654(C→T)突变杂合子，在本中心进行体外受精-胚胎移植和胚胎植入前遗传学诊断。结果 13个胚胎中共有11个胚胎经PCR分析后获得明确诊断，正常胚胎2个(18．1％)；杂合子胚胎6个(54．5％)；双重杂合子胚胎3个(27．3％)。共移植3个胚胎，其中2个正常胚胎、1个杂合子胚胎。在胚胎移植后5周B超示三胎妊娠，孕8周自然减一胎，并于孕20周时经产前诊断，证实均为健康胎儿。现已分娩双胎分别为正常和杂合子。结论 成功应用全基因组扩增技术对β-地中海贫血进行胚胎植入前遗传学诊断，并分娩健康双胎。     

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

We present a new approach to genotyping based on multiplexed shotgun sequencing that can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. We first describe a simple library construction protocol that uses just 10 ng of genomic DNA per individual and makes the approach accessible to any laboratory with standard molecular biology equipment. Sequencing this library results in a large number of sequence reads widely distributed across the genomes of multiplexed bar-coded individuals. We develop a Hidden Markov Model to estimate ancestry at all genomic locations in all individuals using these data. We demonstrate the utility of the approach by mapping a dominant marker allele in D. simulans to within 105 kb of its true position using 96 F1-backcross individuals genotyped in a single lane on an Illumina Genome Analyzer. We further demonstrate the utility of our method by genetically mapping more than 400 previously unassembled D. simulans contigs to linkage groups and by evaluating the quality of targeted introgression lines. At this level of multiplexing and divergence between strains, our method allows estimation of recombination breakpoints to a median of 38-kb intervals. Our analysis suggests that higher levels of multiplexing and/or use of strains with lower levels of divergence are practicable.     

Sequence-based physical mapping of complex genomes by whole genome profiling

We present whole genome profiling (WGP), a novel next-generation sequencing-based physical mapping technology for construction of bacterial artificial chromosome (BAC) contigs of complex genomes, using Arabidopsis thaliana as an example. WGP leverages short read sequences derived from restriction fragments of two-dimensionally pooled BAC clones to generate sequence tags. These sequence tags are assigned to individual BAC clones, followed by assembly of BAC contigs based on shared regions containing identical sequence tags. Following in silico analysis of WGP sequence tags and simulation of a map of Arabidopsis chromosome 4 and maize, a WGP map of Arabidopsis thaliana ecotype Columbia was constructed de novo using a six-genome equivalent BAC library. Validation of the WGP map using the Columbia reference sequence confirmed that 350 BAC contigs (98%) were assembled correctly, spanning 97% of the 102-Mb calculated genome coverage. We demonstrate that WGP maps can also be generated for more complex plant genomes and will serve as excellent scaffolds to anchor genetic linkage maps and integrate whole genome sequence data.     

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

Structural variation (SV) is a rich source of genetic diversity in mammals, but due to the challenges associated with mapping SV in complex genomes, basic questions regarding their genomic distribution and mechanistic origins remain unanswered. We have developed an algorithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences. We applied these methods to two inbred mouse strains: C57BL/6J and DBA/2J. We demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons and segmental duplications; however, our analysis of the C57BL/6J reference strain shows that incomplete reference genome assemblies are a major source of noise. We report 7196 SVs between the two strains, more than two-thirds of which are due to transposon insertions. Of the remainder, 59% are deletions (relative to the reference), 26% are insertions of unlinked DNA, 9% are tandem duplications, and 6% are inversions. To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution. We find that ∼16% of non-transposon SVs have complex breakpoint patterns consistent with template switching during DNA replication or repair, and that this process appears to preferentially generate certain classes of complex variants. Moreover, we find that SVs are significantly enriched in regions of segmental duplication, but that this effect is largely independent of DNA sequence homology and thus cannot be explained by non-allelic homologous recombination (NAHR) alone. This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture.In the six years since the first genome-wide analyses revealed extensive DNA copy number variation (CNV) among human individuals (Iafrate et al. 2004; Sebat et al. 2004), numerous studies have extended this observation in scope and scale with increasingly powerful genomic tools. It is now widely recognized that structural variation (SV), which includes duplications, deletions, inversions, transpositions, and other genomic rearrangements, is an abundant and functionally important class of genetic variation in mammals (Zhang et al. 2009a). Besides the emerging role of inherited variants in complex disease, new structural mutations contribute to sporadic human disorders, are a hallmark of tumor genomes, and drive the evolution of genes and species. For all of these reasons, it is important to generate accurate SV maps in many different organisms and cellular contexts, so that the biological consequences of SV may be assessed, and so that the molecular mechanisms that generate new variation may be fully understood.Several technical challenges have precluded a more complete understanding of the patterns and origins of SV. First, most studies have used array comparative genome hybridization (aCGH), which has limited resolution, cannot detect balanced rearrangements or reconstruct locus architecture, and has limited ability to detect SVs composed of multi-copy elements such as segmental duplications (SDs) or transposable elements (TEs). Second, sequence-based methods such as paired-end mapping (PEM) have emerged as a potent alternative to aCGH (Raphael et al. 2003; Tuzun et al. 2005; Korbel et al. 2007; Lee et al. 2008), but their practical utility has been limited by the high cost of “long-read” sequencing, and the computational difficulties associated with interpreting “short-read” sequence data from complex genomes. Thus, while a number of PEM-based algorithms have been developed to identify SV from short-read sequence data (Chen et al. 2009; Hormozdiari et al. 2009; Korbel et al. 2009; Medvedev et al. 2009) and newer methods have been devised to map SVs at higher resolution (Lee et al. 2009; Sindi et al. 2009), all short-read PEM studies except one (Hormozdiari et al. 2009) have restricted their analyses to paired-end reads that map uniquely to the reference genome. This approach is not ideal given that SVs often involve repeated sequences such as segmental duplications and transposons. Finally, it has been difficult to evaluate structural mutation mechanisms in an unbiased way because genome-wide studies have thus far characterized relatively few breakpoints at single-nucleotide resolution (Korbel et al. 2007; Kidd et al. 2008; Kim et al. 2008; Perry et al. 2008), and the relative contribution of different molecular mechanisms remains a matter of debate.Despite rapid advances in DNA sequencing technologies, affordable and accurate assembly of entire mammalian genomes remains years away. Indeed, even traditional methods have difficulty resolving complex genomic regions. In the interim, we argue that the optimal solution for breakpoint detection is a hybrid approach that combines PEM and local de novo assembly. Here we describe a general approach for unbiased detection, assembly, and mechanistic interpretation of SV breakpoints using both short and long reads, and apply it to whole-genome sequence data from two widely used inbred mouse strains. We show that our algorithms accurately identify diverse classes of SV, capture an unprecedented number of variants, and reveal novel breakpoint features. Of mechanistic significance, we report an abundance of complex SVs that appear to be derived from template switching during DNA replication or repair, and a propensity for duplicated genomic regions to generate new variants through mechanism(s) other than non-allelic homologous recombination (NAHR). A unique strength of this study is our choice of the mouse genome; because the reference genome is derived from an established inbred line (C57BL/6J), we were able to sequence an animal whose genome should be essentially identical to the reference. This important methodological control, which has not been present in any other PEM study, allowed us to distinguish true genetic variation from technical “noise” and poorly assembled genomic regions.     

The genetic differences with whole genome linkage disequilibrium mapping between responder and non-responder in interferon-alpha and ribavirin combined therapy for chronic hepatitis C patients

Interferon-alpha and ribavirin combined therapy has been a mainstream treatment for hepatitis C infection. The efficacy of this combined treatment is around 30% to 60%, and the factors affecting the responsiveness are still poorly defined. Our study is intended to investigate the genetic differences between responder and non-responder patients. The genome-wide linkage disequilibrium screening for loci associated with genetic difference between two patient groups was conducted by using 382 autosomal short tandem repeat (STR) markers involving 92 patients. We have identified 19 STR markers displaying different allele frequencies between the two patient groups. In addition, based on their genomic location and biological function, we selected the CD81 and IL15 genes to perform single nucleotide polymorphism genotyping. In conclusion, this study may provide a new approach for identifying the associated polymorphisms and the susceptible loci for interferon-alpha and ribavirin combined therapy in patients with chronic hepatitis C.     

Tissue-specific extinguisher loci in the murine genome: A screening study based on a rat/mouse microcell hybrid panel

Extinction of tissue-specific traits in intertypic somatic cell hybrids is a well-known phenomenon. In the past few years, microcell hybrids have been used in attempts to dissect this phenotype genetically, and tissue-specific extinguisher loci have been mapped to two different mouse chromosomes. When transferred from fibroblasts into hepatoma cells by microcell fusion, these loci down-regulate expression of specific liver genes intrans. However, other liver genes that are extinguished in genotypically complete hybrids seem not to be extinguished in monochromosomal hybrids. To assess the generality of monochromosomal extinction phenotypes, we assembled a collection of rat hepatoma/mouse fibroblast microcell hybrids that represent most of the mouse chromosome complement, and we screened them for expression of a large number of liver-specific genes. Phosphoenolpyruvate carboxykinase gene expression was down-regulated in hybrids containing mouse chromosome 7 or mouse chromosome 11, but other extinction phenotypes were not readily apparent. These results indicate that extinction of many liver genes may be a polygenic trait.     

Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing

In clinical diagnostics, both array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping have proven to be powerful genomic technologies utilized for the evaluation of developmental delay, multiple congenital anomalies, and neuropsychiatric disorders. Differences in the ability to resolve genomic changes between these arrays may constitute an implementation challenge for clinicians: which platform (SNP vs array CGH) might best detect the underlying genetic cause for the disease in the patient? While only SNP arrays enable the detection of copy number neutral regions of absence of heterozygosity (AOH), they have limited ability to detect single-exon copy number variants (CNVs) due to the distribution of SNPs across the genome. To provide comprehensive clinical testing for both CNVs and copy-neutral AOH, we enhanced our custom-designed high-resolution oligonucleotide array that has exon-targeted coverage of 1860 genes with 60 000 SNP probes, referred to as Chromosomal Microarray Analysis – Comprehensive (CMA-COMP). Of the 3240 cases evaluated by this array, clinically significant CNVs were detected in 445 cases including 21 cases with exonic events. In addition, 162 cases (5.0%) showed at least one AOH region >10 Mb. We demonstrate that even though this array has a lower density of SNP probes than other commercially available SNP arrays, it reliably detected AOH events >10 Mb as well as exonic CNVs beyond the detection limitations of SNP genotyping. Thus, combining SNP probes and exon-targeted array CGH into one platform provides clinically useful genetic screening in an efficient manner.     

Recommendations for whole genome sequencing in diagnostics for rare diseases

In 2016, guidelines for diagnostic Next Generation Sequencing (NGS) have been published by EuroGentest in order to assist laboratories in the implementation and accreditation of NGS in a diagnostic setting. These guidelines mainly focused on Whole Exome Sequencing (WES) and targeted (gene panels) sequencing detecting small germline variants (Single Nucleotide Variants (SNVs) and insertions/deletions (indels)). Since then, Whole Genome Sequencing (WGS) has been increasingly introduced in the diagnosis of rare diseases as WGS allows the simultaneous detection of SNVs, Structural Variants (SVs) and other types of variants such as repeat expansions. The use of WGS in diagnostics warrants the re-evaluation and update of previously published guidelines. This work was jointly initiated by EuroGentest and the Horizon2020 project Solve-RD. Statements from the 2016 guidelines have been reviewed in the context of WGS and updated where necessary. The aim of these recommendations is primarily to list the points to consider for clinical (laboratory) geneticists, bioinformaticians, and (non-)geneticists, to provide technical advice, aid clinical decision-making and the reporting of the results.Subject terms: Next-generation sequencing, Medical genetics     

Toward mapping the biology of the genome

This issue of Genome Research presents new results, methods, and tools from The ENCODE Project (ENCyclopedia of DNA Elements), which collectively represents an important step in moving beyond a parts list of the genome and promises to shape the future of genomic research. This collection sheds light on basic biological questions and frames the current debate over the optimization of tools and methodological challenges necessary to compare and interpret large complex data sets focused on how the genome is organized and regulated. In a number of instances, the authors have highlighted the strengths and limitations of current computational and technical approaches, providing the community with useful standards, which should stimulate development of new tools. In many ways, these papers will ripple through the scientific community, as those in pursuit of understanding the "regulatory genome" will heavily traverse the maps and tools. Similarly, the work should have a substantive impact on how genetic variation contributes to specific diseases and traits by providing a compendium of functional elements for follow-up study. The success of these papers should not only be measured by the scope of the scientific insights and tools but also by their ability to attract new talent to mine existing and future data.     

A new strategy for mapping the human genome.

Recent advances in agarose gel electrophoresis of large DNA fragments raise the possibility of an entirely new approach to mapping mammalian genomes. In this article is discussed the potential of this technology for tackling problems such as construction of linkage maps, identifying chromosome translocation breakpoints, and moving from linked markers to genes causing diseases such as the muscular dystrophies and Huntington's chorea.     

Genetic inducible fate mapping in mouse: establishing genetic lineages and defining genetic neuroanatomy in the nervous system.

A fascinating aspect of developmental biology is how organs are assembled in three dimensions over time. Fundamental to understanding organogenesis is the ability to determine when and where specific cell types are generated, the lineage of each cell, and how cells move to reside in their final position. Numerous methods have been developed to mark and follow the fate of cells in various model organisms used by developmental biologists, but most are not readily applicable to mouse embryos in utero because they involve physical marking of cells through injection of tracers. The advent of sophisticated transgenic and gene targeting techniques, combined with the use of site-specific recombinases, has revolutionized fate mapping studies in mouse. Furthermore, using genetic fate mapping to mark cells has opened up the possibility of addressing fundamental questions that cannot be studied with traditional methods of fate mapping in other organisms. Specifically, genetic fate mapping allows both the relationship between embryonic gene expression and cell fate (genetic lineage) to be determined, as well as the link between gene expression domains and anatomy (genetic anatomy) to be established. In this review, we present the ever-evolving development of genetic fate mapping techniques in mouse, especially the recent advance of Genetic Inducible Fate Mapping. We then review recent studies in the nervous system (focusing on the anterior hindbrain) as well as in the limb and with adult stem cells to highlight fundamental developmental processes that can be discovered using genetic fate mapping approaches. We end with a look toward the future at a powerful new approach that combines genetic fate mapping with cellular phenotyping alleles to study cell morphology, physiology, and function using examples from the nervous system.     

Diagnostic whole genome sequencing and split‐read mapping for nucleotide resolution breakpoint identification in CNTNAP2 deficiency syndrome

Whole genome sequencing (WGS) has the potential to report on all types of genetic abnormality, thus converging diagnostic testing on a single methodology. Although WGS at sufficient depth for robust detection of point mutations is still some way from being affordable for diagnostic purposes, low‐coverage WGS is already an excellent method for detecting copy number variants (“CNVseq”). We report on a family in which individuals presented with a presumed autosomal recessive syndrome of severe intellectual disability and epilepsy. Array comparative genomic hybridization (CGH) analysis had revealed a homozygous deletion apparently lying within intron 3 of CNTNAP2. Since this was too small for confirmation by FISH, CNVseq was used, refining the extent of this mutation to approximately 76.8 kb, encompassing CNTNAP2 exon 3 (an out‐of‐frame deletion). To characterize the precise breakpoints and provide a rapid molecular diagnostic test, we resequenced the CNVseq library at medium coverage and performed split read mapping. This yielded information for a multiplex polymerase chain reaction (PCR) assay, used for cascade screening and/or prenatal diagnosis in this family. This example demonstrates a rapid, low‐cost approach to converting molecular cytogenetic findings into robust PCR‐based tests. © 2014 The Authors. American Journal of Medical Genetics Part A Published by Wiley Periodicals, Inc.     

Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190 562 genetic variations in the human genome

To construct an infrastructure for genome-wide association studies of common diseases or drug sensitivities, we have been systematically exploring common variants by resequencing genomic regions containing genes in DNA from 24 Japanese individuals. We have analyzed a total of 154 Mb, corresponding to approximately 5% of the human genome, and so far have identified 174 269 single-nucleotide polymorphisms and 16 293 insertion/deletion polymorphisms within gene regions, i.e., one polymorphism in 807 bp on average. Our data are freely available via our web site (http://snp.ims.u-tokyo.ac.jp) and will facilitate studies to identify genes associated with susceptibility to common diseases and genes involved in sensitivity to therapeutic drugs. Received: August 22, 2002 / Accepted: August 27, 2002 Acknowledgments We are grateful to the members of our SNP discovery team for providing us with a high degree of experimental expertise. This work was supported by a grant from the Japanese Millennium Project. Correspondence to:Y. Nakamura     

Development of a panel of monochromosomal somatic cell hybrids for rapid gene mapping

We have assembled a panel of monochromosomal somatic cell hybrids for use in gene mapping. DNA from each individual hybrid was used as a probe on normal human metaphases to identify the human chromosome and any fragments by reverse painting. To test the efficiency of the panel PCR amplification of DNA from the monochromosomal somatic cell hybrid panel was used in combination with human specific oligonucleotide primers to assign α-catenin (CTNNA1) and p21/WAFl to chromosomes 5 and 6 respectively. These genes were localized further using hybrids containing specific translocations to 5qll-qter and 6p21 respectively. We also developed primers to enable us to assign 17 ESTs sequenced by the HGMP Resource Centre. The hybrid panel was developed with support of the UK HGMP and the DNA is available to all registered users.     

Development of a whole blood intracellular cytokine staining assay for mapping CD4(+) and CD8(+) T-cell responses across the HIV-1 genome

A whole blood peptide mapping intracellular cytokine staining (ICS) assay was developed that allows the direct comparison, at the individual peptide level, of CD4(+) and CD8(+) T-cell responses that span every encoded protein, in patients infected with HIV-1. Whole blood samples from HIV-1 infected patients were stimulated with overlapping synthetic peptides spanning nine subtype C HIV-1 gene regions (Gag, Pol, Nef, Env, Tat, Rev, Vif, Vpu, Vpr). Following stimulation and permeabilization, cells were stained with fluorochrome labelled antibodies to CD3, CD8 (CD4(+) cells were defined as CD8 negative cells), and IL-2 and IFN-gamma. A total of 396 overlapping peptides were arranged in pools with a matrix design which allowed the identification of individual peptide responses from multiple pool responses. HIV-1 infected patients screened using this method showed a broad range of peptide responses across the entire HIV-1 genome with CD8 T-cell responses being higher in frequency in magnitude than CD4(+) T-cell responses. The advantages of this whole blood ICS assay include the following: (1) the response to all potential HIV-1 epitopes across the genome can be examined, (2) the responding cell type can be monitored in the same reaction, and (3) considerably less blood is required than would be necessary if peripheral blood mononuclear cells (PBMC) were first isolated prior to peptide stimulation.     

Expanded genetic screening panel for the Ashkenazi Jewish population

PurposeCarrier screening programs that identify the presence of known mutations have been effective for reducing the incidence of autosomal recessive conditions in the Ashkenazi Jewish (AJ) population and other populations. Yet, these programs have not realized their full potential. Furthermore, many known autosomal recessive and dominant conditions are not screened for and the molecular basis of other conditions for which screening might be offered is unknown.MethodsThrough literature review and annotation of full sequenced genomes from healthy individuals, we expanded the list of mutations. Mutations were identified in a sample of 128 fully sequenced AJ genomes that were filtered through clinical databases and curated manually for clinical validity and utility using the American College of Medical Genetics and Genomics scoring (ACMG) system. Other known mutations were identified through literature review.ResultsA panel of 163 mutations was identified for 76 autosomal recessive, 24 autosomal dominant, and 3 X-linked disorders.ConclusionScreening for a broader range of disorders not only could further reduce the incidence of autosomal recessive disorders but also could offer the benefits of early or presymptomatic diagnosis.