Whole Exome Sequencing Reveals the Genetic Basis of a Case of Idiopathic Hemolytic Anemia and Suggests Candidate Rare Variants for ADHD in a Utah Pedigree

poste

The Implementation of Clinical Genomics: Ethical, Societal and Regulatory Considerations.

As the cost of next-generation sequencing continues to decrease exponentially, it is becoming both affordable and relatively easy for laboratories outside of large-scale sequencing centers to perform exon capture and eventually whole genome sequencing in selected individuals. However, the current genomics system lacks a systematic way to deliver results to participants, even in matters of life and death, as we have discovered in some of our recent research1,2. There is substantial debate in the medical genetics and ethics communities concerning whether genomic data originating from research can or should be returned to participants or not, and, if so, under what conditions. The exponential increase in human genetic information is shining a spotlight on the problems with how researchers handle and process human genomic information. Specifically, researchers are largely unable to share the information that arises from their sequencing efforts with participants – without whom, the research wouldn’t be possible. At the moment, human genetics researchers operate in a totally unregulated environment, following their own protocols to obtain, store, track, and analyze DNA – creating many opportunities for samples to be mixed up, or other errors. Researchers take shortcuts to save time and money, given that most never expect (as did I) that their results might actually directly impact the unique life of another human being. Here, I present two real-world scenarios from our own research highlighting the issues involved (1,2). I am suggesting that we change the way we collect and process samples for human genetics research. I argue that we should create a formalized protocol akin to the rigorous process doctors and other healthcare workers go through during any clinical lab test, practically eliminating the chances of mistakes and mix-ups. An added benefit is that sharing the genomic data with research participants will allow them the opportunity to share their own data with other researchers and citizen scientists, thus allowing for potentially faster and easier replication of published results. We cannot forget the wise words of the late Charles Epstein, from his 2001 William Allan award lecture: “the operative word in ‘human genetics’ is ‘human.’ Human genetics is about human beings—about humanity and humaneness.” (3

Whole Genome Sequencing Analysis of an Idiopathic Intellectual Disability Syndrome

We present a new idiopathic intellectual disability syndrome accompanied with distinctive facial dysmorphology. X-chromosome inactivation assays reveal skewing in the mother, suggesting the possibility of an X-linked disorder. High-density genotyping arrays were performed on both children revealing no known causal or pathogenic SNVs and no known CNVs that might contribute to the phenotype. Whole genome sequencing was performed with Complete Genomics and subsequent sequence analysis led to the identification of severa

Genome-wide linkage using the Social Responsiveness Scale in Utah autism pedigrees

<p>Abstract</p> <p>Background</p> <p>Autism Spectrum Disorder<b>s </b>(ASD) are phenotypically heterogeneous, characterized by impairments in the development of communication and social behaviour and the presence of repetitive behaviour and restricted interests. Dissecting the genetic complexity of ASD may require phenotypic data reflecting more detail than is offered by a categorical clinical diagnosis. Such data are available from the Social Responsiveness Scale (SRS) which is a continuous, quantitative measure of social ability giving scores that range from significant impairment to above average ability.</p> <p>Methods</p> <p>We present genome-wide results for 64 multiplex and extended families ranging from two to nine generations. SRS scores were available from 518 genotyped pedigree subjects, including affected and unaffected relatives. Genotypes from the Illumina 6 k single nucleotide polymorphism panel were provided by the Center for Inherited Disease Research. Quantitative and qualitative analyses were done using MCLINK, a software package that uses Markov chain Monte Carlo (MCMC) methods to perform multilocus linkage analysis on large extended pedigrees.</p> <p>Results</p> <p>When analysed as a qualitative trait, linkage occurred in the same locations as in our previous affected-only genome scan of these families, with findings on chromosomes 7q31.1-q32.3 [heterogeneity logarithm of the odds (HLOD) = 2.91], 15q13.3 (HLOD = 3.64), and 13q12.3 (HLOD = 2.23). Additional positive qualitative results were seen on chromosomes 6 and 10 in regions that may be of interest for other neuropsychiatric disorders. When analysed as a quantitative trait, results replicated a peak found in an independent sample using quantitative SRS scores on chromosome 11p15.1-p15.4 (HLOD = 2.77). Additional positive quantitative results were seen on chromosomes 7, 9, and 19.</p> <p>Conclusions</p> <p>The SRS linkage peaks reported here substantially overlap with peaks found in our previous affected-only genome scan of clinical diagnosis. In addition, we replicated a previous SRS peak in an independent sample. These results suggest the SRS is a robust and useful phenotype measure for genetic linkage studies of ASD. Finally, analyses of SRS scores revealed linkage peaks overlapping with evidence from other studies of neuropsychiatric diseases. The information available from the SRS itself may, therefore, reveal locations for autism susceptibility genes that would not otherwise be detected.</p

Toward more accurate variant calling for “personal genomes”

To date, researchers and clinicians use widely different methods for detecting and reporting human genetic variation. As the size of academic and private databases grow and as the use of the existing genomic techniques expand, researchers and clinicians stand to greatly benefit from the standardization of data generating approaches and analysis methodologies. To successfully implement genomic analyses in the clinic, it will be critically important to optimize the existing pipelines for attaining a higher sensitivity and specificity for more accurate and consistent variant calling

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

BACKGROUND: To facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for variant calling are available, but it is unclear how comparable these tools are or what their relative merits in real-world scenarios might be. METHODS: We sequenced 15 exomes from four families using commercial kits (Illumina HiSeq 2000 platform and Agilent SureSelect version 2 capture kit), with approximately 120X mean coverage. We analyzed the raw data using near-default parameters with five different alignment and variant-calling pipelines (SOAP, BWA-GATK, BWA-SNVer, GNUMAP, and BWA-SAMtools). We additionally sequenced a single whole genome using the sequencing and analysis pipeline from Complete Genomics (CG), with 95% of the exome region being covered by 20 or more reads per base. Finally, we validated 919 single-nucleotide variations (SNVs) and 841 insertions and deletions (indels), including similar fractions of GATK-only, SOAP-only, and shared calls, on the MiSeq platform by amplicon sequencing with approximately 5000X mean coverage. RESULTS: SNV concordance between five Illumina pipelines across all 15 exomes was 57.4%, while 0.5 to 5.1% of variants were called as unique to each pipeline. Indel concordance was only 26.8% between three indel-calling pipelines, even after left-normalizing and intervalizing genomic coordinates by 20 base pairs. There were 11% of CG variants falling within targeted regions in exome sequencing that were not called by any of the Illumina-based exome analysis pipelines. Based on targeted amplicon sequencing on the MiSeq platform, 97.1%, 60.2%, and 99.1% of the GATK-only, SOAP-only and shared SNVs could be validated, but only 54.0%, 44.6%, and 78.1% of the GATK-only, SOAP-only and shared indels could be validated. Additionally, our analysis of two families (one with four individuals and the other with seven), demonstrated additional accuracy gained in variant discovery by having access to genetic data from a multi-generational family. CONCLUSIONS: Our results suggest that more caution should be exercised in genomic medicine settings when analyzing individual genomes, including interpreting positive and negative findings with scrutiny, especially for indels. We advocate for renewed collection and sequencing of multi-generational families to increase the overall accuracy of whole genomes

Southeast Asia and the Politics of Vulnerability

The economic and political crises that have recently engulfed the countries of Southeast Asia provide a stark reminder of just how difficult the challenge of sustained regional development remains. In retrospect, the hyperbole that surrounded the 'East Asian miracle' looks overblown, and testimony to the manner in which rhetoric can outstrip reality, especially in the minds of international investors. Certainly, some observers had questioned the depth and resilience of capitalist development in Southeast Asia, but in the years immediately prior to 1997 such analyses tended to be in the minority. Now, of course, it is painfully obvious that much of Southeast Asia's economic and political development was extremely fragile. When seen in historical context, this outcome should not have been surprising since the countries of modern Southeast Asia, both as independent nations and as colonies of various imperial powers, have been highly vulnerable to the actions of powerful external political and economic forces. This paper will examine the economic bases and the political consequences of this vulnerablity, both domestically and at a regional level. I argue that the recent crisis has served as an unwelcome reminder of just how constrained, dependent and vulnerable the Southeast Asia region's development prospects remain, a situation that is exacerbated by, and which contributes to, domestic political crises

Searching for gravitational waves from known pulsars

We present upper limits on the amplitude of gravitational waves from 28 isolated pulsars using data from the second science run of LIGO. The results are also expressed as a constraint on the pulsars' equatorial ellipticities. We discuss a new way of presenting such ellipticity upper limits that takes account of the uncertainties of the pulsar moment of inertia. We also extend our previous method to search for known pulsars in binary systems, of which there are about 80 in the sensitive frequency range of LIGO and GEO 600.Comment: Accepted by CQG for the proceeding of GWDAW9, 7 pages, 2 figure

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss)

BACKGROUND: Comparative genomics, through the integration of genetic maps from species of interest with whole genome sequences of other species, will facilitate the identification of genes affecting phenotypes of interest. The development of microsatellite markers from expressed sequence tags will serve to increase marker densities on current salmonid genetic maps and initiate in silico comparative maps with species whose genomes have been fully sequenced. RESULTS: Eighty-nine polymorphic microsatellite markers were generated for rainbow trout of which at least 74 amplify in other salmonids. Fifty-five have been associated with functional annotation and 30 were mapped on existing genetic maps. Homologous sequences were identified for 20 of the EST containing microsatellites to identify comparative assignments within the tetraodon, mouse, and/or human genomes. CONCLUSION: The addition of microsatellite markers constructed from expressed sequence tag data will facilitate the development of high-density genetic maps for rainbow trout and comparative maps with other salmonids and better studied species