10x Genomics
Chromium Genome & Exome
Long Ranger2.1 (latest), printed on 11/23/2024
Phasing BRCA1/BRCA2
| Analysis software for 10x Genomics linked read products is no longer supported. Raw data processing pipelines and visualization tools are available for download and can be used for analyzing legacy data from 10x Genomics kits in accordance with our end user licensing agreement without support. |
BRCA1 and BRCA2 are tumor suppressor genes that encode proteins involved in DNA repair. When either of these proteins is not functional DNA damage may not be repaired properly which increases the risk of cancer. BRCA1 and BRCA2 mutations are linked to an increased risk of breast cancer, ovarian cancer, prostate cancer, and pancreatic cancer.
To explore variant phasing of BRCA1 and BRCA2 enter the gene names into the search bar in Loupe. Genome coordinates will replace the gene names in the search bar after pressing enter and the view will switch to HAPLOTYPES by default. On the HAPLOTYPES view both genes will be displayed as separate tracks as seen in the example below.
Phased variants are displayed in a haplotype aware format shown as HAPLOTYPE 1 (top) and HAPLOTYPE 2 (bottom). Stretches of variants phased together are called phase blocks that are outlined in black. In the example below there are pairs of variants that are in cis (top) and trans (bottom). Inactivating mutations in trans disable both copies of a gene whereas mutations in cis have a wild type copy of the gene.
To investigate a variant select the SNP and SNP Details dialog box will appear on the right. In the benign example below, the SNP located at chr17:41,234,470 (A>G) is a silent mutation.
