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We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health and cognition in a community sample of 7100 unrelated children and youth of European or East Asian ancestry (Spit for Science). Clinically significant or susceptibility CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of attention-deficit/hyperactivity disorder (ADHD) traits (P = 5.0 × 10−3), longer response inhibition (a cognitive deficit found in several mental health and neurodevelopmental disorders; P = 1.0 × 10−2) and increased prevalence of mental health diagnoses (P = 1.9 × 10−6, odds ratio: 3.09), specifically ADHD, autism spectrum disorder anxiety and learning problems/learning disorder (P’s

Defining different genetic subtypes of autism spectrum disorder (ASD) can enable the prediction of developmental outcomes. Based on minor physical and major congenital anomalies, we categorize 325 Canadian children with ASD into dysmorphic and nondysmorphic subgroups. We develop a method for calculating a patient-level, genome-wide rare variant score (GRVS) from whole-genome sequencing (WGS) data. GRVS is a sum of the number of variants in morphology-associated coding and non-coding regions, weighted by their effect sizes. Probands with dysmorphic ASD have a significantly higher GRVS compared to those with nondysmorphic ASD (P = 0.03). Using the polygenic transmission disequilibrium test, we observe an over-transmission of ASD-associated common variants in nondysmorphic ASD probands (P = 2.9 × 10−3). These findings replicate using WGS data from 442 ASD probands with accompanying morphology data from the Simons Simplex Collection. Our results provide support for an alternative genomic classification of ASD subgroups using morphology data, which may inform intervention protocols.

We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health, and cognitive biomarkers in a community sample of 7,100 unrelated European, and East Asian children and youth (Spit for Science). Diagnoses of mental health disorders were found in 17.5% of participants and 27.6% scored in the highest 10% on either or both ADHD and OCD trait measures. Clinically relevant CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of ADHD (p=5.0×10−3), on a cognitive biomarker of mental health (response inhibition (p=1.0×10−2)), and on prevalence of mental disorders (p=1.9×10−6, odds ratio: 3.09). With a rise of mental illness, our data establishes a baseline for delineating genetic contributors in paediatric-onset conditions.One Sentence SummaryCopy number variation predicts neurodevelopmental and mental health phenotypes in the general population.

Fully understanding the genetic factors involved in Autism Spectrum Disorder (ASD) requires whole-genome sequencing (WGS), which theoretically allows the detection of all types of genetic variants. With the aim of generating an unprecedented resource for resolving the genomic architecture underlying ASD, we analyzed genome sequences and phenotypic data from 5,100 individuals with ASD and 6,212 additional parents and siblings (total n=11,312) in the Autism Speaks MSSNG Project, as well as additional individuals from other WGS cohorts. WGS data and autism phenotyping were based on high-quality short-read sequencing (>30x coverage) and clinically accepted diagnostic measures for ASD, respectively. For initial discovery of ASD-associated genes, we used exonic sequence-level variants from MSSNG as well as whole-exome sequencing-based ASD data from SPARK and the Autism Sequencing Consortium (>18,000 trios plus additional cases and controls), identifying 135 ASD-associated protein-coding genes with false discovery rate SCN2A and a nuclear mitochondrial insertion impacting SYNGAP1. Polygenic risk scores did not differ between children with ASD in multiplex families versus simplex, and rare, damaging recessive events were significantly depleted in multiplex families, collectively suggesting that rare, dominant variation plays a predominant role in multiplex ASD. Our study provides a guidebook for exploring genotype-phenotype correlations in the 15-20% of ASD families who carry ASD-associated rare variants, as well as an entry point to the larger and more diverse studies that will be required to dissect the etiology in the >80% of the ASD population that remains idiopathic. All data resulting from this study are available to the medical genomics research community in an open but protected manner.

Funding Information: This work was supported by the National Institute of Mental Health/U.S. Army Medical Research and Development Command (Grant No. R01MH106595 [to CMN, MBS, KJRe, and KCK]), and National Institutes of Health (Grant No. 5U01MH109539 [to the Psychiatric Genomics Consortium] and Grant No. U19 MH069056 [to BWD])). Financial support for the PTSD PGC was provided by the Cohen Veterans Bioscience, Stanley Center for Psychiatric Research at the Broad Institute, and One Mind. Genotyping of samples was provided in part through the Stanley Center for Psychiatric Genetics at the Broad Institute supported by Cohen Veterans Bioscience Statistical analyses were carried out on the LISA/Genetic Cluster Computer ( https://userinfo.surfsara.nl/systems/lisa ) hosted by SURFsara. This research has been conducted using the UK Biobank resource (Application No. 41209). Posttraumatic stress disorder (PTSD) is a heritable (h2 = 24–71%) psychiatric illness. Copy number variation (CNV) is a form of rare genetic variation that has been implicated in the etiology of psychiatric disorders, but no large-scale investigation of CNV in PTSD has been performed. We present an association study of CNV burden and PTSD symptoms in a sample of 114,383 participants (13,036 cases and 101,347 controls) of European ancestry. CNVs were called using two calling algorithms and intersected to a consensus set. Quality control was performed to remove strong outlier samples. CNVs were examined for association with PTSD within each cohort using linear or logistic regression analysis adjusted for population structure and CNV quality metrics, then inverse variance weighted meta-analyzed across cohorts. We examined the genome-wide total span of CNVs, enrichment of CNVs within specified gene-sets, and CNVs overlapping individual genes and implicated neurodevelopmental regions. The total distance covered by deletions crossing over known neurodevelopmental CNV regions was significant (beta = 0.029, SE = 0.005, P = 6.3 × 10−8). The genome-wide neurodevelopmental CNV burden identified explains 0.034% of the variation in PTSD symptoms. The 15q11.2 BP1-BP2 microdeletion region was significantly associated with PTSD (beta = 0.0206, SE = 0.0056, P = 0.0002). No individual significant genes interrupted by CNV were identified. 22 gene pathways related to the function of the nervous system and brain were significant in pathway analysis (FDR q < 0.05), but these associations were not significant once NDD regions were removed. A larger sample size, better detection methods, and annotated resources of CNV are needed to explore this relationship further. publishersversion published

Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.

Defining different genetic subtypes of autism spectrum disorder (ASD) can enable the prediction of developmental outcomes. Based on minor physical and major congenital anomalies, we categorized 325 Canadian children with ASD into dysmorphic and nondysmorphic subgroups. We developed a method for calculating a patient-level, genome-wide rare variant score (GRVS) from whole-genome sequencing (WGS) data. GRVS is a sum of the number of variants in morphology-associated coding and non-coding regions, weighted by their effect sizes. Probands with dysmorphic ASD had a significantly higher GRVS compared to those with nondysmorphic ASD (P= 0.027). Using the polygenic transmission disequilibrium test, we observed an over-transmission of ASD-associated common variants in nondysmorphic ASD probands (P= 2.9×10−3). These findings replicated using WGS data from 442 ASD probands with accompanying morphology data from the Simons Simplex Collection. Our results provide support for an alternative genomic classification of ASD subgroups using morphology data, which may inform intervention protocols.

BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant. RESULTS: Whole genome sequencing of the first 56 participants identified 207 662 805 sequence variants and 27 494 copy number variations. We analyzed a prioritized disease-associated data set (n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants — associated with cancer, cardiac or neurodegenerative phenotypes — remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual. INTERPRETATION: Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care.

The majority of the heredity of melanoma remains unexplained, however inherited copy number changes have not yet been systematically studied. The genetic environment is highly relevant to treatment stratification, and new gene discovery is therefore desirable. Using an unbiased whole genome screening approach for copy number we identify here a novel melanoma predisposing factor, familial duplications of genePPP2R3B, encoding a regulatory unit of critical phosphatase PP2A. Significant correlation between expression ofPPP2R3Bin tumour tissue and survival in a large melanoma cohort was confirmed, and associated with a non-immunological expression profile. Mechanistically, construction and extensive characterization of a stable, inducible cellular model forPPP2R3Boverexpression revealed induction of pigment cell switching towards proliferation and away from migration. Importantly, this was independent of the known microphthalmia-associated transcription factor(MITF)-controlled pigment cell phenotype switch, and was instead driven by uncharacterised geneC21orf91. Bioinformatic studies point toC21orf91as a novel target ofMITF,and therefore a potential hub in the control of phenotype switching in melanoma. This study identifies novel germline copy number variants inPPP2R3Bpredisposing to melanocytic neoplasia, and uncovers a new potential therapeutic targetC21orf91in the control of pigment cell proliferation.

Purpose Hemiplegia is a subtype of cerebral palsy (CP) in which one side of the body is affected. Our earlier study of unselected children with CP demonstrated de novo and clinically relevant rare inherited genomic copy-number variations (CNVs) in 9.6% of participants. Here, we examined the prevalence and types of CNVs specifically in hemiplegic CP. Methods We genotyped 97 unrelated probands with hemiplegic CP and their parents. We compared their CNVs to those of 10,851 population controls, in order to identify rare CNVs (

A major contribution to the genome variability among individuals comes from deletions and duplications - collectively termed copy number variations (CNVs) - which alter the diploid status of DNA. These alterations may have no phenotypic effect, account for adaptive traits or can underlie disease. We have compiled published high-quality data on healthy individuals of various ethnicities to construct an updated CNV map of the human genome. Depending on the level of stringency of the map, we estimated that 4.8-9.5% of the genome contributes to CNV and found approximately 100 genes that can be completely deleted without producing apparent phenotypic consequences. This map will aid the interpretation of new CNV findings for both clinical and research applications.

A remaining hurdle to whole-genome sequencing (WGS) becoming a first-tier genetic test has been accurate detection of copy-number variations (CNVs). Here, we used several datasets to empirically develop a detailed workflow for identifying germline CNVs >1 kb from short-read WGS data using read depth-based algorithms. Our workflow is comprehensive in that it addresses all stages of the CNV-detection process, including DNA library preparation, sequencing, quality control, reference mapping, and computational CNV identification. We used our workflow to detect rare, genic CNVs in individuals with autism spectrum disorder (ASD), and 120/120 such CNVs tested using orthogonal methods were successfully confirmed. We also identified 71 putative genic de novo CNVs in this cohort, which had a confirmation rate of 70%; the remainder were incorrectly identified as de novo due to false positives in the proband (7%) or parental false negatives (23%). In individuals with an ASD diagnosis in which both microarray and WGS experiments were performed, our workflow detected all clinically relevant CNVs identified by microarrays, as well as additional potentially pathogenic CNVs < 20 kb. Thus, CNVs of clinical relevance can be discovered from WGS with a detection rate exceeding microarrays, positioning WGS as a single assay for genetic variation detection.

Background Rare Copy Number Variants (CNVs) likely play an important role in common childhood neuropsychiatric disorders such as ADHD and OCD. These disorders represent the extremes of broadly distributed behavioural traits that are influenced by underlying variation in fundamental cognitive processes such as response inhibition. Using behavioural and cognitive trait-based approaches in population samples can help reduce heterogeneity and improve power to detect rare CNVs associated with these disorders. Currently we do not know the prevalence of CNVs related to neuropsychiatric disorders in youth in the general population. Using the Spit for Science sample (Toronto, Canada), we examined the association of rare CNVs with ADHD, OCD and response inhibition traits. Methods We collected DNA and quantitative trait measures from 16,718 youth (ages 6–17 years) at a local science museum. We measured ADHD traits using the Strengths and Weaknesses of ADHD and Normal Behavior (SWAN) scale, obsessive-compulsive traits using the Toronto Obsessive-Compulsive scale (TOCS) and response inhibition, a putative endophenotype for ADHD, using the Stop-Task. We genotyped unrelated Caucasians (n=5,320) using Illumina HumanCoreExome beadchips. CNVs were called using three algorithms: iPattern (ipn), PennCNV (pcnv), and QuantiSNP (qsnp) and a high confidence dataset was generated by retaining variants detected by two or more algorithms and at least 10 kb in size. We defined rare variants as those with less than 0.1% frequency against our population controls. Using linear regression, we examined whether CNV burden, overall and within psychiatrically relevant gene sets (e.g., brain expression, synaptic function), is associated with response inhibition, ADHD and OCD traits. Results After stringent quality control, 4815 (90.5%) of participants remained with a total of 9,490 rare CNVs (1.97/individual on average). We observed CNVs affecting 23 genomic loci previously implicated in neurodevelopmental conditions (e.g. 22q11.2) in 59 (1.2%) of participants. Other large CNVs affecting known psychiatric genes (e.g., ASTN2, NRXN1) were also identified. Significantly more deletions (>500 kb; p=0.04) and enrichment of deletions in genes involved in synapse structure, neuron projection and neurophenotypes in mice (p Discussion In a large pediatric general population sample, brain-related CNVs were associated with neuropsychiatric traits in children although the pattern of enrichment differed between ADHD, OCD and response inhibition. Our results replicate several previous CNV burden findings for ADHD and OCD suggesting a similar genetic architecture between traits and disorders. Our approach shows the feasibility of CNV analysis and quality of CNV data from the HumanCoreExome array in a large population based sample.

IMMP2L, the gene encoding the inner mitochondrial membrane peptidase subunit 2-like protein, has been reported as a candidate gene for Tourette syndrome, autism spectrum disorder (ASD) and additional neurodevelopmental disorders. Here we genotyped 100 trio families with an index proband with autism spectrum disorder in Han Chinese population and found three cases with rare exonic IMMP2L deletions. We have conducted a comprehensive meta-analysis to quantify the association of IMMP2L deletions with ASD using 5,568 cases and 10,279 controls. While the IMMP2L deletions carried non-recurrent breakpoints, in contrast to previous reports, our meta-analysis found no evidence of association (P > 0.05) between IMMP2L deletions and ASD. We also observed common exonic deletions impacting IMMP2L in a separate control (5,971 samples) cohort where subjects were screened for psychiatric conditions. This is the first systematic review and meta-analysis regarding the effect of IMMP2L deletions on ASD, but further investigations in different populations, especially Chinese population may be still needed to confirm our results.

We have systematically compared copy number variant (CNV) detection on eleven microarrays to evaluate data quality and CNV calling, reproducibility, concordance across array platforms and laboratory sites, breakpoint accuracy and analysis tool variability. Different analytic tools applied to the same raw data typically yield CNV calls with

Numerous types of DNA variation exist, ranging from SNPs to larger structural alterations such as copy number variants (CNVs) and inversions. Alignment of DNA sequence from different sources has been used to identify SNPs1,2 and intermediate-sized variants (ISVs)3. However, only a small proportion of total heterogeneity is characterized, and little is known of the characteristics of most smaller-sized (1.5 million SNPs. Some differences were simple insertions and deletions, but in regions containing CNVs, segmental duplication and repetitive DNA, they were more complex. Our results uncover substantial undescribed variation in humans, highlighting the need for comprehensive annotation strategies to fully interpret genome scanning and personalized sequencing projects.

Background Genetics play an important role in ADHD and OCD but only a handful of mostly common risk variants have been identified in studies that compare ADHD/OCD patients with healthy controls. Copy number variants of high penetrance may play an important role in childhood neuropsychiatric disorders. Our current knowledge of CNVs in ADHD and OCD is based on relatively small samples of patients, and to interpret the significance of these CNVs we need to assess risk CNVs in the general population. To this end we determine the frequency of clinically relevant CNVs in a large population based sample of children and adolescents and examined the association of rare CNVs with ADHD and OCD traits. Methods Quantitative data on ADHD traits using the Strengths and Weaknesses of ADHD and Normal Behavior (SWAN) scale and OC traits using the Toronto Obsessive-Compulsive scale (TOCS) was collected from 17,263 youth (ages 6-17 years) from the community. We genotyped unrelated Caucasians (n=5,366) and East Asians (n=989) using Illumina HumanCoreExome beadchips. CNV were called using three algorithms: iPattern (ipn), PennCNV (pcnv), and QuantiSNP (qsnp) and a high confidence dataset was generated by retaining variants detected by two or more algorithms and at least 10kb in size. We defined rare variants as those with less than 0.1% frequency against our population controls. We plan to examine whether CNV burden, overall and within psychiatrically relevant gene sets (e.g., brain expression, brain development), is associated with ADHD and OCD traits. We will also test if individual CNVs are associated with ADHD and OCD traits. Results After stringent quality control, 4857 (90.5%) Caucasian and 933 (94.3%) East Asian samples remained. Total number of CNVs was 31,798 with a mean size of 117,316 base pairs and a maximum size of 7.1 MB. The average number of CNVs per participants was 6. We uncovered 9,836 rare variants, of which 4,151 are deletions and 5,687 are duplications. This comprises of 7,613 rare CNVs from European subjects (mean size = 139,856 kb) and 2,225 from Asian individuals (mean size =123,141 kb). This represented a mean of 1.57 and 2.38 rare CNVs per individuals, respectively. We identified a total of 15 different known genomic disorders from 41 subjects (0.7%) in this cohort. Quantitative trait results forthcoming. Discussion Our novel approach will help elucidate the rate of psychiatrically relevant CNVs in the general population and the association of these CNVs with ADHD and OCD. Our preliminary data shows the feasibility of CNV analysis and quality of CNV data from the HumanCoreExome array in a large population based sample. Financial Relationships I (or my spouse/partner) do have potential conflicts of interest to disclose.

Chromosomal microarray analysis to assess copy-number variation has become a first-tier genetic diagnostic test for individuals with unexplained neurodevelopmental disorders or multiple congenital anomalies. More than 100 cytogenetic laboratories worldwide use the new ultra-high resolution Affymetrix CytoScan-HD array to genotype hundreds of thousands of samples per year. Our aim was to develop a copy-number variation resource from a new population sample that would enable more accurate interpretation of clinical genetics data on this microarray platform and others. Genotyping of 1,000 adult volunteers who are broadly representative of the Ontario population (as obtained from the Ontario Population Genomics Platform) was performed with the CytoScan-HD microarray system, which has 2.7 million probes. Four independent algorithms were applied to detect copy-number variations. Reproducibility and validation metrics were quantified using sample replicates and quantitative-polymerase chain reaction, respectively. DNA from 873 individuals passed quality control and we identified 71,178 copy-number variations (81 copy-number variations/individual); 9.8% (6,984) of these copy-number variations were previously unreported. After applying three layers of filtering criteria, from our highest confidence copy-number variation data set we obtained >95% reproducibility and >90% validation rates (73% of these copy-number variations overlapped at least one gene). The genotype data and annotated copy-number variations for this largely Caucasian population will represent a valuable public resource enabling clinical genetics research and diagnostics. Genet Med 17 9, 747–752.

Even with significant advances in technology, few studies of structural variation have yet resolved to the level of the precise nucleotide junction. We examined the sequence of 408,532 gains, 383,804 losses, and 166 inversions from the first sequenced personal genome, to quantify the relative proportion of mutational mechanisms. Among small variants (1 kb), we observed that 72.6% of them were associated with nonhomologous processes and 24.9% with microsatellites events. Medium-size variants (10 kb) were commonly related to minisatellites (25.8%) and retrotransposons (24%), whereas 46.2% of large variants (10 kb) were associated with nonallelic homologous recombination. We genotyped eight new breakpoint-resolved inversions at (3q26.1, Xp11.22, 7q11.22, 16q23.1, 4q22.1, 1q31.3, 6q27, and 16q24.1) in human populations to elucidate the structure of these presumed benign variants. Three of these inversions (3q26.1, 7q11.22, and 16q23.1) were accompanied by unexpected complex rearrangements. In particular, the 16q23.1 inversion and an accompanying deletion would create conjoined chymotrypsinogen genes (CTRB1 and CTRB2), disrupt their gene structure, and exhibit differentiated allelic frequencies among populations. Also, two loci (Xp11.3 and 6q27) of potential reference assembly orientation errors were found. This study provides a thorough account of formation mechanisms for structural variants, and reveals a glimpse of the dynamic structure of inversions.

Background There are four known pericentromeric euchromatic variants of chromosome 9 in the literature that are increasingly being observed in diagnostic cytogenetic laboratories. These variants pose diagnostic and counselling dilemmas, especially in prenatal settings, as distinction of a pathogenic alteration from a euchromatic variant is difficult. The molecular characterisation of three of these four variants has been reported. In this study, the genomic structure of the fourth variant, an additional G-positive band at 9q13-q21, is characterised. Methods Two unrelated families with the 9q13-q21 duplication variant, and a third individual with a cytogenetically visible 9q13-q21 deletion, were studied using conventional and molecular cytogenetics techniques, as well as microarrays. The highly repetitive nature of the segmental duplications in the region also necessitated the use of both interphase and metaphase fluorescence in situ hybridisation (FISH). Results It was determined that the DNA that constitutes this variant was ∼15–20 megabases in size and tandemly repeated as 3–4 cassettes of intrachromosomal segmental duplication. The variant appeared constitutively similar in sequence content and organisation between the two unrelated individuals, and it was inherited without apparent change. Sequences found amplified in the two duplication carriers were absent in the carrier of the deletion variant. Conclusions The sequences involved in both the 9q13-q21 duplication and deletion appear the same, implying reciprocity and suggesting non-allelic homologous recombination as the underlying mechanism. All four known euchromatic variants of chromosome 9 have now been shown to encompass segmental duplications. Importantly, a set of validated FISH probes was defined for the detection and characterisation of this 9q13-q21 amplification in the context of other chromosome 9 variants, allowing apparently benign variants to be distinguished from pathogenic changes.

The term monoclonal B-cell lymphocytosis (MBL) is used to characterize individuals with a circulating population of clonal B-cells and no other features of a lymphoproliferative disorder. Although several recent studies have examined the molecular basis of this condition, the subgroup of MBL lacking CD5 expression has been largely overlooked. In this study, we sequenced a t(2;7) in a patient with persistent but non-progressing CD5 − MBL. This revealed a breakpoint at 2p11.2 localized to the recombination signal sequence (RSS) of the immunoglobulin κ ( IGK ) variable gene IGKV3-15 , and a breakpoint at 7q21.2 located 520 base pairs (bp) upstream of the transcription start site of cyclin-dependent kinase 6 ( CDK6 ). The 7q breakpoint showed perfect sequence homology to the immunoglobulin RSS heptamer, and was located within 3 bp of a t(2;7) junction previously characterized in splenic marginal zone lymphoma (SMZL). These findings highlight a genetic link between CD5 − MBL and SMZL, and implicate the dysregulation of CDK6 in the emergence of this preclinical disorder.

Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.

The aim of this chapter is to provide instruction for analyzing and mapping recent segmental and gene duplications in eukaryotic genomes. We describe a bioinformatics-based approach utilizing computational tools to manage eukaryotic genome sequences to characterize and understand the evolutionary fates and trajectories of duplicated genes. An introduction to bioinformatics tools and programs such as BLAST, Perl, BioPerl, and the GFF specification provides the necessary background to complete this analysis for any eukaryotic genome of interest.

The aim of this chapter is to provide instruction for analyzing and mapping recent segmental and gene duplications in eukaryotic genomes. We describe a bioinformatics-based approach utilizing computational tools to manage eukaryotic genome sequences to characterize and understand the evolutionary fates and trajectories of duplicated genes. An introduction to bioinformatics tools and programs such as BLAST, Perl, BioPerl, and the GFF specification provides the necessary background to complete this analysis for any eukaryotic genome of interest.

7 páginas, 2 figuras, 1 tabla., We have identified C7orf11, which localizes to the nucleus and is expressed in fetal hair follicles, as the first disease gene for nonphotosensitive trichothiodystrophy (TTD). C7orf11 maps to chromosome 7p14, and the disease locus has been designated “TTDN1” (TTDnonphotosensitive 1). Mutations were found in patients with Amish brittle-hair syndrome and in other nonphotosensititive TTD cases with mental retardation and decreased fertility but not in patients with Sabinas syndrome or Pollitt syndrome. Therefore, genetic heterogeneity in nonphotosensitive TTD is a feature similar to that observed in photosensitive TTD, which is caused by mutations in transcription factor II H (TFIIH) subunit genes. Comparative immunofluorescence analysis, however, suggests that C7orf11 does not influence TFIIH directly. Given the absence of cutaneous photosensitivity in the patients with C7orf11 mutations, together with the protein’s nuclear localization, C7orf11 may be involved in transcription but not DNA repair., We acknowledge The Centre for Applied Genomics, the Genome Canada/Ontario Genome Institute, the Hospital for Sick Children Foundation, the Association Française contre les Myopathies, and the Dykstra Foundation in Detroit (grant to C.E.J.). S.W.S. is an Investigator of the Canadian Institutes of Health Research, a Scholar of the McLaughlin Centre for Molecular Medicine, and an International Scholar of the Howard Hughes Medical Institute.

BLAST-based computational heuristics were used to identify large and recent segmental duplications in the mouse genome sequence. Here a database of recently duplicated regions of the mouse genome is presented., Background The high quality of the mouse genome draft sequence and its associated annotations are an invaluable biological resource. Identifying recent duplications in the mouse genome, especially in regions containing genes, may highlight important events in recent murine evolution. In addition, detecting recent sequence duplications can reveal potentially problematic regions of the genome assembly. We use BLAST-based computational heuristics to identify large (≥ 5 kb) and recent (≥ 90% sequence identity) segmental duplications in the mouse genome sequence. Here we present a database of recently duplicated regions of the mouse genome found in the mouse genome sequencing consortium (MGSC) February 2002 and February 2003 assemblies. Results We determined that 33.6 Mb of 2,695 Mb (1.2%) of sequence from the February 2003 mouse genome sequence assembly is involved in recent segmental duplications, which is less than that observed in the human genome (around 3.5-5%). From this dataset, 8.9 Mb (26%) of the duplication content consisted of 'unmapped' chromosome sequence. Moreover, we suspect that an additional 18.5 Mb of sequence is involved in duplication artifacts arising from sequence misassignment errors in this genome assembly. By searching for genes that are located within these regions, we identified 675 genes that mapped to duplicated regions of the mouse genome. Sixteen of these genes appear to have been duplicated independently in the human genome. From our dataset we further characterized a 42 kb recent segmental duplication of Mater, a maternal-effect gene essential for embryogenesis in mice. Conclusion Our results provide an initial analysis of the recently duplicated sequence and gene content of the mouse genome. Many of these duplicated loci, as well as regions identified to be involved in potential sequence misassignment errors, will require further mapping and sequencing to achieve accuracy. A Genome Browser database was set up to display the identified duplication content presented in this work. This data will also be relevant to the growing number of investigators who use the draft genome sequence for experimental design and analysis.

Objective To develop a novel clinical test using microarray technology as a high-resolution alternative to current methods for detection of known and novel microdeletions on the Y chromosome. Design Custom Agilent 8x15K array comparative genomic hybridization (aCGH) with 10,162 probes on an average probe spacing of 2.5 kb across the euchromatic region of the Y chromosome. Setting Clinical diagnostic laboratory. Patient(s) Men with infertility (n = 104) and controls with proven fertility (n = 148). Intervention(s) Microarray genotyping of DNA. Main Outcome Measure(s) Gene copy number variation determined by log ratio of probe signal intensity against a DNA reference. Result(s) Our aCGH experiments found all known AZF microdeletions as well as additional unbalanced structural alterations. In addition to complete AZF microdeletions, we found that AZFc partial deletions represent a risk factor for male infertility. In total, aCGH-based detection achieved a diagnostic yield of ∼11% and also revealed additional potentially etiologic copy number variations requiring further characterization. Conclusion(s) The aCGH approach is a reliable high-resolution alternative to multiplex polymerase chain reaction for the discovery of pathogenic chromosome Y microdeletions in male infertility.

Abstract 1191 Efforts to decipher the biological basis of lymphoid malignancy have recently been accentuated by the discovery of clonal B-cells in otherwise healthy individuals, an entity now referred to as monoclonal B-cell lymphocytosis (MBL). However, while considerable attention has been devoted towards characterizing this pervasive condition, the subgroup of MBL lacking CD5 expression has been largely overlooked. To address this imbalance, our group previously examined a series of cases presenting with persistent but non-progressing CD5- clonal lymphocytosis (Amato D et al, Am J Clin Pathol 2007). Herein, karyotypic analysis revealed a unique case harboring the translocation t(2;7)(p11;q22), a genetic abnormality which has been documented in association with splenic marginal zone lymphoma (SMZL). The present study set out to further characterize the t(2;7) breakpoint of this novel case study in order to test whether the translocation represents a common genetic link between CD5- MBL and SMZL. Using fluorescent in situ hybridization (FISH), the breakpoint on chromosome 7 was initially narrowed down to a 41 kilobase (kb) candidate region at 7q21.2, as inferred by a split signal from the cosmid probe cos130a6. Based on the proximity of the chromosome 2 breakpoint to the immunoglobulin kappa (IGK) locus on 2p11, long-range polymerase chain reaction (L-PCR) was subsequently performed according to the hypothesis that the t(2;7) translocation had arisen from aberrant VJ recombination. Primers targeting conserved sequences within the IGK variable genes were sequentially juxtaposed with primers on chromosome 7 located at 6 kb intervals across the 41 kb candidate region, and L-PCR conducted using both patient and reference DNA as a template. This process gave rise to a single instance of strong patient-specific amplification, thereby indicating successful targeting of the t(2;7) breakpoint. Sanger sequencing of the corresponding PCR product confirmed this result, revealing a breakpoint at 2p11.2 localized to the heptamer recombination signal sequence (RSS) of the IGK variable gene V3-15, alongside a breakpoint at 7q21.2 located 3.6 kb upstream of the transcription start site of the cell cycle regulator cyclin dependent kinase 6 (CDK6). Remarkably, the breakpoint on chromosome 7 showed perfect sequence homology to the immunoglobulin RSS heptamer, and was within 3 base pairs of a breakpoint previously characterized in association with SMZL (Corcoran M et al, Oncogene 1999). Hence, this result implicates the dysregulation of CDK6 during the clonal expansion observed in CD5- MBL, and highlights the potential role of aberrant VJ recombination during the formation of this genetic abnormality. By establishing a clear genetic link between CD5- MBL and SMZL, this study supports the notion of CD5- MBL as a precursor of overt malignancy within a ‘multi-hit’ model of oncogenesis. Finally, the sequence-level characterization of a novel translocation breakpoint by L-PCR strongly validates the potential utility of this approach during future studies of immunoglobulin-associated translocations. Disclosures: No relevant conflicts of interest to declare.

The high quality of the mouse genome draft sequence and its associated annotations are an invaluable biological resource. Identifying recent duplications in the mouse genome, especially in regions containing genes, may highlight important events in recent murine evolution. In addition, detecting recent sequence duplications can reveal potentially problematic regions of the genome assembly. We use BLAST-based computational heuristics to identify large (≥ 5 kb) and recent (≥ 90% sequence identity) segmental duplications in the mouse genome sequence. Here we present a database of recently duplicated regions of the mouse genome found in the mouse genome sequencing consortium (MGSC) February 2002 and February 2003 assemblies. We determined that 33.6 Mb of 2,695 Mb (1.2%) of sequence from the February 2003 mouse genome sequence assembly is involved in recent segmental duplications, which is less than that observed in the human genome (around 3.5-5%). From this dataset, 8.9 Mb (26%) of the duplication content consisted of 'unmapped' chromosome sequence. Moreover, we suspect that an additional 18.5 Mb of sequence is involved in duplication artifacts arising from sequence misassignment errors in this genome assembly. By searching for genes that are located within these regions, we identified 675 genes that mapped to duplicated regions of the mouse genome. Sixteen of these genes appear to have been duplicated independently in the human genome. From our dataset we further characterized a 42 kb recent segmental duplication of Mater, a maternal-effect gene essential for embryogenesis in mice. Our results provide an initial analysis of the recently duplicated sequence and gene content of the mouse genome. Many of these duplicated loci, as well as regions identified to be involved in potential sequence misassignment errors, will require further mapping and sequencing to achieve accuracy. A Genome Browser database was set up to display the identified duplication content presented in this work. This data will also be relevant to the growing number of investigators who use the draft genome sequence for experimental design and analysis.

In 4 1/2 years (July 1973 to December 1977), 28 thoracotomies were performed by emergency physicians in the emergency department of a 540-bed community hospital, which averaged 25,800 visits per year. Two patients had sustained crush injuries of the chest in traffic accidents, and 26 had penetrating chest and/or abdominal trauma. Twenty-three of the patients had no vital signs and were clinically dead on arrival. Of these, four (17%) were resuscitated and transported to the operating room; three (13%) were long-term survivors and two left the hospital with no serious sequelae. The other five patients arrived with some vital signs but subsequently had cardiopulmonary arrests in the emergency department. Three (60%) were initially resuscitated using thoracotomy and transported to the operating room but there were no long-term survivors among this group of five. Of the 28 patients who underwent thoracotomies in the emergency department, one in four (7/28; 25%) were initially resuscitated, and one in nine (3/28; 11%) were long-term survivors. Thoracotomy in a community hospital emergency department by emergency physicians can be life-saving.

This study compares two similar groups of patients in cardiopulmonary arrest with ventricular fibrillation (VF). In the survival study group of 296 patients, 148 patients received an endotracheal tube airway (ETA) and 148 patients received an esophageal gastric tube airway (EGTA), the improved version of the esophageal obturator airway (EOA). Survival rates, both short term (ETA = 35.8%, EGTA = 39.1%) and long term (ETA = 11.5%, EGTA = 16.2%), and neurological sequelae of survivors showed no statistically significant difference between the two groups (P greater than .05). In addition, we found that success and complication rates of intubation were similar. Training time was longer for the ETA. We conclude that both airways have a place in the prehospital setting.

Widespread utilization of angiography has allowed discovery of fibromuscular hyperplasia affecting medium-sized arteries throughout the body. Such arterial dysplasia of the carotid and vertebral arteries is rare. However, as experience accumulates, it is becoming increasingly evident that this may be an important entity in these locations. Its significance derives from the fact that it may produce cerebral ischemia or infarction in persons of any age. The fact that this condition is frequently associated with intracerebral aneurysms and with fibromuscular hyperplasia of the renal artery suggests that it is a generalized arterial abnormality of common etiology. This communication details the clinical aspects of five patients with fibromuscular hyperplasia of the carotid and vertebral arteries. In one instance, this condition affected the vertebral arteries, in three, the carotids alone, and one, both the carotids and the vertebrals. The object of this presentation is to emphasize the diverse symptomatology, the association with other