@article {908, title = {Multiplexed Functional Assessment of Genetic Variants in CARD11.}, journal = {Am J Hum Genet}, volume = {107}, year = {2020}, month = {2020 12 03}, pages = {1029-1043}, abstract = {

Genetic testing has increased the number of variants identified in disease genes, but the diagnostic utility is limited by lack of understanding variant function. CARD11 encodes an adaptor protein that expresses dominant-negative and gain-of-function variants associated with distinct immunodeficiencies. Here, we used a "cloning-free" saturation genome editing approach in a diploid cell line to simultaneously score 2,542 variants for decreased or increased function in the region of CARD11 associated with immunodeficiency. We also described an exon-skipping mechanism for CARD11 dominant-negative activity. The classification of reported clinical variants was sensitive (94.6\%) and specific (88.9\%), which rendered the data immediately useful for interpretation of seven coding and splicing variants implicated in immunodeficiency found in our clinic. This approach is generalizable for variant interpretation in many other clinically actionable genes, in any relevant cell type.

}, keywords = {Adenine, B-Cell CLL-Lymphoma 10 Protein, B-Lymphocytes, CARD Signaling Adaptor Proteins, Cell Line, Diploidy, Exons, Genes, Dominant, Genetic Variation, Guanylate Cyclase, Humans, Immunologic Deficiency Syndromes, Jurkat Cells, Lymphoma, NF-kappa B p50 Subunit, Piperidines, Polymorphism, Single Nucleotide, Primary Immunodeficiency Diseases, Sensitivity and Specificity}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2020.10.015}, author = {Meitlis, Iana and Allenspach, Eric J and Bauman, Bradly M and Phan, Isabelle Q and Dabbah, Gina and Schmitt, Erica G and Camp, Nathan D and Torgerson, Troy R and Nickerson, Deborah A and Bamshad, Michael J and Hagin, David and Luthers, Christopher R and Stinson, Jeffrey R and Gray, Jessica and Lundgren, Ingrid and Church, Joseph A and Butte, Manish J and Jordan, Mike B and Aceves, Seema S and Schwartz, Daniella M and Milner, Joshua D and Schuval, Susan and Skoda-Smith, Suzanne and Cooper, Megan A and Starita, Lea M and Rawlings, David J and Snow, Andrew L and James, Richard G} } @article {177, title = {Assessing structural variation in a personal genome-towards a human reference diploid genome.}, journal = {BMC Genomics}, volume = {16}, year = {2015}, month = {2015 Apr 11}, pages = {286}, abstract = {

BACKGROUND: Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods.

RESULTS: We demonstrate Parliament{\textquoteright}s efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8\%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus.

CONCLUSIONS: HS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.

}, keywords = {Computational Biology, Databases, Genetic, Diploidy, Genome, Human, Genomic Structural Variation, Humans, Sequence Analysis, DNA, Software}, issn = {1471-2164}, doi = {10.1186/s12864-015-1479-3}, author = {English, Adam C and Salerno, William J and Hampton, Oliver A and Gonzaga-Jauregui, Claudia and Ambreth, Shruthi and Ritter, Deborah I and Beck, Christine R and Davis, Caleb F and Dahdouli, Mahmoud and Ma, Singer and Carroll, Andrew and Veeraraghavan, Narayanan and Bruestle, Jeremy and Drees, Becky and Hastie, Alex and Lam, Ernest T and White, Simon and Mishra, Pamela and Wang, Min and Han, Yi and Zhang, Feng and Stankiewicz, Pawel and Wheeler, David A and Reid, Jeffrey G and Muzny, Donna M and Rogers, Jeffrey and Sabo, Aniko and Worley, Kim C and Lupski, James R and Boerwinkle, Eric and Gibbs, Richard A} }