Publications by authors named "Joe Whitney"
Article Synopsis
- Autism spectrum disorder (ASD) prevalence in Qatar is around 1.1%, but genetic research in the region is limited; the BARAKA-Qatar Study aims to create a biorepository for ASD families to facilitate future research.
- * Whole-genome sequencing (WGS) analysis of 100 families revealed potentially pathogenic variants in 27% of them, with a notable contribution from dominant and homozygous variants, particularly in consanguineous families.
- * The study also identified 28 new candidate genes related to ASD, emphasizing the importance of including under-represented populations in genetic research to understand the disorder better.
Article Synopsis
- Phasing of heterozygous alleles is essential for interpreting the effects of genetic variations related to cystic fibrosis (CF), and researchers sequenced 477 CF individuals to construct haplotypes using linked-read sequencing.
- The resulting haplotypes are visualized in an interactive web app called CFTbaRcodes, allowing for exploration of complex CF gene variations.
- Fine-mapping revealed that a specific 20-kb deletion and a missense variant are linked to an increased risk of CF-related meconium ileus and pancreatic issues, providing insights into the genetic mechanisms involved in both CF and non-CF pancreatitis.
Article Synopsis
- Full understanding of autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS), highlighted by the latest Autism Speaks MSSNG resource that includes data from over 11,000 individuals.
- The study found ASD-associated rare genetic variants in about 14% of individuals with ASD, examining data from MSSNG and the Simons Simplex Collection, which suggests similar prevalence in both datasets.
- The identified variants were mostly nuclear (98%) with a small fraction being mitochondrial, and the research aims to help explore genetic links to ASD traits and identify causes for the 85% of ASD cases that currently lack identified genetic causes.
Population sequencing often requires collaboration across a distributed network of sequencing centers for the timely processing of thousands of samples. In such massive efforts, it is important that participating scientists can be confident that the accuracy of the sequence data produced is not affected by which center generates the data. A study was conducted across three established sequencing centers, located in Montreal, Toronto, and Vancouver, constituting Canada's Genomics Enterprise (www.
View Article and Find Full Text PDFThe genetic basis of autism spectrum disorder (ASD) is known to consist of contributions from de novo mutations in variant-intolerant genes. We hypothesize that rare inherited structural variants in cis-regulatory elements (CRE-SVs) of these genes also contribute to ASD. We investigated this by assessing the evidence for natural selection and transmission distortion of CRE-SVs in whole genomes of 9274 subjects from 2600 families affected by ASD.
View Article and Find Full Text PDFArticle Synopsis
- The Personal Genome Project Canada focuses on collecting and sharing data from whole genome sequencing alongside health information from volunteers, starting with an initial group of 56 participants.
- The study identified a vast number of genetic variants, including over 207 million sequence variants and nearly 28,000 copy number variations, revealing potential health implications for 25% of those involved.
- Findings included pathogenic variants, risk factors for various conditions, and a significant number of recessive disease alleles, highlighting the potential for whole genome sequencing to uncover important medical insights for participants, despite being primarily for research access.
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.
View Article and Find Full Text PDFWe are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.
View Article and Find Full Text PDFRecent Hits Acquired by BLAST (ReHAB): a tool to identify new hits in sequence similarity searches.
BMC Bioinformatics
February 2005
Background: Sequence similarity searching is a powerful tool to help develop hypotheses in the quest to assign functional, structural and evolutionary information to DNA and protein sequences. As sequence databases continue to grow exponentially, it becomes increasingly important to repeat searches at frequent intervals, and similarity searches retrieve larger and larger sets of results. New and potentially significant results may be buried in a long list of previously obtained sequence hits from past searches.
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