PacBio Announces a New Informatics Analysis Method for Highly Homologous Genes

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[{"type":"text","content":"Paraphase Enables Researchers to Analyze Genes That are Critically Relevant but Hard to Genotype\nMENLO PARK, Calif., March 14, 2023 /PRNewswire/ -- PacBio (NASDAQ: PACB), a leading developer of highly accurate sequencing solutions, today announced a new informatics method that genotypes gene paralogs and pseudogenes with high accuracy. The new computational tool, named \"Paraphase,\" enables variant calling, copy number analysis and phasing by identifying the full gene sequence of each of the haplotypes for all genes and pseudogenes of the same gene family. Many medically relevant genes fall into segmental duplications and thus have highly similar gene family members or pseudogenes. The sequence similarity often leads to error prone read alignment and variant calling.\n\n \n \n \n \n \n \n\n \n\"Through the use of Paraphase, we are able to identify the full sequence of each copy of a gene and, importantly, identify the number of functional and non-functional copies of a gene,\" said Mike Eberle, Vice President of Computational Biology at PacBio. \"This will allow researchers to conduct more accurate carrier analyses and provide a framework for studying the underlying genetics of these complex genomic regions. We believe that applying this method to larger, diverse, population data will ultimately enable researchers to better understand medically important problems, such as silent carriers for spinal muscular atrophy.\"\nParaphase has been used on several medically relevant genes with highly similar paralogs or pseudogenes, including, CYP21A2 (21-hydroxylase-deficient congenital adrenal hyperplasia), TNXB (Ehlers-Danlos syndrome), STRC (hereditary hearing loss and deafness) and SMN1 and 2 (spinal muscular atrophy). SMN1 is >99.9 percent similar in sequence to its paralog, SMN2, and both genes have variable copy numbers across populations. Mutations in SMN1 cause spinal muscular atrophy (SMA), a leading cause of early infant death.\nHigh throughput detailed sequence analysis of complete genes is challenging using existing technologies, and identifying silent carriers (having two copies of SMN1 on one chromosome and zero copies on the other, accounting for 27 percent of carriers in African populations) is impossible without pedigree information. In a recent peer-reviewed publication, Paraphase was able to detect these pathogenic v...

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