CONTRA: copy number analysis for targeted resequencing

Li, Jason; Lupat, Richard; Amarasinghe, Kaushalya; Thompson, Ella R.; Doyle, Maria A.; Ryland, Georgina L; Tothill, Richard W.; Halgamuge, Saman K.; Campbell, Ian; Gorringe, Kylie L.

doi:10.1093/bioinformatics/bts146

Cited by 298 publications

(248 citation statements)

References 19 publications

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“…Nevertheless, this algorithm is time-processor-consuming and, therefore, other software such as CONTRA should offer an interesting alternative. 30 A major advantage of the NGS procedure is that the progressive implementation of specific software should allow the detection of other types of alterations, which are not found by using conventional procedures. For instance, complex rearrangements, such as inversions, should be detected taking advantage of paired-end data, by using software such as PINDEL.…”

Section: Discussionmentioning

confidence: 99%

Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes

et al. 2014

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To optimize the molecular diagnosis of hereditary breast and ovarian cancer (HBOC), we developed a next-generation sequencing (NGS)-based screening based on the capture of a panel of genes involved, or suspected to be involved in HBOC, on pooling of indexed DNA and on paired-end sequencing in an Illumina GAIIx platform, followed by confirmation by Sanger sequencing or MLPA/QMPSF. The bioinformatic pipeline included CASAVA, NextGENe, CNVseq and Alamut-HT. We validated this procedure by the analysis of 59 patients' DNAs harbouring SNVs, indels or large genomic rearrangements of BRCA1 or BRCA2. We also conducted a blind study in 168 patients comparing NGS versus Sanger sequencing or MLPA analyses of BRCA1 and BRCA2. All mutations detected by conventional procedures were detected by NGS. We then screened, using three different versions of the capture set, a large series of 708 consecutive patients. We detected in these patients 69 germline deleterious alterations within BRCA1 and BRCA2, and 4 TP53 mutations in 468 patients also tested for this gene. We also found 36 variations inducing either a premature codon stop or a splicing defect among other genes: 5/708 in CHEK2, 3/708 in RAD51C, 1/708 in RAD50, 7/708 in PALB2, 3/708 in MRE11A, 5/708 in ATM, 3/708 in NBS1, 1/708 in CDH1, 3/468 in MSH2, 2/468 in PMS2, 1/708 in BARD1, 1/468 in PMS1 and 1/468 in MLH3. These results demonstrate the efficiency of NGS in performing molecular diagnosis of HBOC. Detection of mutations within other genes than BRCA1 and BRCA2 highlights the genetic heterogeneity of HBOC. In BRCA1 and BRCA2 mutation carriers, the cumulative risk of breast cancer at 70 years has been estimated to 65 and 45%, respectively, and the risk of ovarian cancer to 39 and 10%, respectively. 3 The identification of a deleterious BRCA1/BRCA2 mutation within a family is crucial for the medical follow-up, as mutation carriers should be offered annual MRI or, alternatively, prophylactic mastectomy and prophylactic salpingooophorectomy. Furthermore, in a breast cancer patient, the detection of a germline BRCA1 or BRCA2 mutation may have important therapeutic consequences: complete mastectomy instead of partial mastectomy and, in the future, the prescription of specific targeted therapies, such as PARP inhibitors. 4,5 Considering the medical consequences of the identification of a germline BRCA1 or BRCA2 mutation and the frequency of mutation carriers, which has

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Section: Discussionmentioning

confidence: 99%

Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes

et al. 2014

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“…Sequence variation was identified using multiple software tools to capture the full spectrum of DNA variation; singlenucleotide polymorphisms and small (o10 base pairs) insertions and deletions (indels) were determined using samtools 31 (http://samtools.sourceforge.net) to ensure a low false-positive rate; larger indels (410 base pairs) were identified using Pindel 32 (https:// trac.nbic.nl/pindel); translocations were identified using Breakdancer 33 (http://breakdancer.sourceforge. net); and copy number variation was identified using CONTRA 34 (http://contra-cnv.sourceforge.net). Sequence variants were then annotated using the SeattleSeq annotation server (http://gvsbatch.gs.…”

Section: Discussionmentioning

confidence: 99%

Retinoblastoma gene mutations detected by whole exome sequencing of Merkel cell carcinoma

et al. 2014

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Merkel cell carcinoma is a highly aggressive cutaneous neuroendocrine tumor that has been associated with Merkel cell polyomavirus in up to 80% of cases. Merkel cell polyomavirus is believed to influence pathogenesis, at least in part, through expression of the large T antigen, which includes a retinoblastoma protein-binding domain. However, there appears to be significant clinical and morphological overlap between polyomaviruspositive and polyomavirus-negative Merkel cell carcinoma cases. Although much of the recent focus of Merkel cell carcinoma pathogenesis has been on polyomavirus, the pathogenesis of polyomavirus-negative cases is still poorly understood. We hypothesized that there are underlying human somatic mutations that unify Merkel cell carcinoma pathogenesis across polyomavirus status, and to investigate we performed whole exome sequencing on five polyomavirus-positive cases and three polyomavirus-negative cases. We found that there were no significant differences in the overall number of single-nucleotide variations, copy number variations, insertion/deletions, and chromosomal rearrangements when comparing polyomavirus-positive to polyomavirus-negative cases. However, we did find that the retinoblastoma pathway genes harbored a high number of mutations in Merkel cell carcinoma. Furthermore, the retinoblastoma gene (RB1) was found to have nonsense truncating protein mutations in all three polyomavirus-negative cases; no such mutations were found in the polyomavirus-positive cases. In all eight cases, the retinoblastoma pathway dysregulation was confirmed by immunohistochemistry. Although polyomavirus-positive Merkel cell carcinoma is believed to undergo retinoblastoma dysregulation through viral large T antigen expression, our findings demonstrate that somatic mutations in polyomavirus-negative Merkel cell carcinoma lead to retinoblastoma dysregulation through an alternative pathway. This novel finding suggests that the retinoblastoma pathway dysregulation leads to an overlapping Merkel cell carcinoma phenotype and that oncogenesis occurs through either a polyomavirusdependent (viral large T antigen expression) or polyomavirus-independent (host somatic mutation) mechanism. Modern Pathology (2014) 27, 1073-1087; doi:10.1038/modpathol.2013.235; published online 10 January 2014Keywords: Merkel cell carcinoma; retinoblastoma; whole exome sequencing; polyomavirus Merkel cell carcinoma is a rare neuroendocrine tumor of the skin with an aggressive clinical course and an increased prevalence in the elderly and immunosuppressed. 1 The incidence of Merkel cell carcinoma has increased in the last several decades, and the United States has an estimated incidence rate of 0.32 per 100 000 persons per year. 2 Merkel cell carcinoma has a predilection for sun exposed areas, most often occurring in the head and neck region. 3 There is an overall 5-year survival rate of 40%, with stage being a significant prognosticator. 3,4 Merkel cell polyomavirus was discovered in Merkel cell carcinoma and found to be clonally integ...

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“…Since deletions generate genotypic signatures identical to isodisomy, this step is essential to prevent the unintentional ascription of deletions as UPD. With the availability of tools to detect CNVs from SNP genotyping and exome data (Love et al 2011;Fromer et al 2012;Li et al 2012; P Vijayarangakannan, T Fitzgerald, C Joyce, S McCarthy, ME Hurles, pers. comm.…”

Section: Discussionmentioning

confidence: 99%

A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders

et al. 2013

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Exome sequencing of parent-offspring trios is a popular strategy for identifying causative genetic variants in children with rare diseases. This method owes its strength to the leveraging of inheritance information, which facilitates de novo variant calling, inference of compound heterozygosity, and the identification of inheritance anomalies. Uniparental disomy describes the inheritance of a homologous chromosome pair from only one parent. This aberration is important to detect in genetic disease studies because it can result in imprinting disorders and recessive diseases. We have developed a software tool to detect uniparental disomy from child–mother–father genotype data that uses a binomial test to identify chromosomes with a significant burden of uniparentally inherited genotypes. This tool is the first to read VCF-formatted genotypes, to perform integrated copy number filtering, and to use a statistical test inherently robust for use in platforms of varying genotyping density and noise characteristics. Simulations demonstrated superior accuracy compared with previously developed approaches. We implemented the method on 1057 trios from the Deciphering Developmental Disorders project, a trio-based rare disease study, and detected six validated events, a significant enrichment compared with the population prevalence of UPD (1 in 3500), suggesting that most of these events are pathogenic. One of these events represents a known imprinting disorder, and exome analyses have identified rare homozygous candidate variants, mainly in the isodisomic regions of UPD chromosomes, which, among other variants, provide targets for further genetic and functional evaluation.

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CONTRA: copy number analysis for targeted resequencing

Cited by 298 publications

References 19 publications

Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes

Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes

Retinoblastoma gene mutations detected by whole exome sequencing of Merkel cell carcinoma

A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders

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