Title | Searching thousands of genomes to classify somatic and novel structural variants using STIX. |
Publication Type | Journal Article |
Year of Publication | 2022 |
Authors | Chowdhury, M, Pedersen, BS, Sedlazeck, FJ, Quinlan, AR, Layer, RM |
Journal | Nat Methods |
Volume | 19 |
Issue | 4 |
Pagination | 445-448 |
Date Published | 2022 Apr |
ISSN | 1548-7105 |
Keywords | Algorithms, Genome, Genomic Structural Variation, High-Throughput Nucleotide Sequencing, Humans, Neoplasms, Software |
Abstract | Structural variants are associated with cancers and developmental disorders, but challenges with estimating population frequency remain a barrier to prioritizing mutations over inherited variants. In particular, variability in variant calling heuristics and filtering limits the use of current structural variant catalogs. We present STIX, a method that, instead of relying on variant calls, indexes and searches the raw alignments from thousands of samples to enable more comprehensive allele frequency estimation. |
DOI | 10.1038/s41592-022-01423-4 |
Alternate Journal | Nat Methods |
PubMed ID | 35396485 |
PubMed Central ID | PMC9007735 |
Grant List | R00 HG009532 / HG / NHGRI NIH HHS / United States R01 HG010757 / HG / NHGRI NIH HHS / United States U01 CA231978 / CA / NCI NIH HHS / United States |
Searching thousands of genomes to classify somatic and novel structural variants using STIX.
Similar Publications
Deep sequencing of candidate genes identified 14 variants associated with smoking abstinence in an ethnically diverse sample. Sci Rep. 2024;14(1):6385. | .
FAIR Header Reference genome: a TRUSTworthy standard. Brief Bioinform. 2024;25(3). | .
Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes. Circ Res. 2024;134(7):842-854. | .