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Hi, I'm working on a rare Mendelian disease next-gen sequencing project. We expect our disease to have recessive mutations. The second-gen sequence data is doing a great job of finding variants (well SNPs, indels are ish and CNVs I think are a lost cause due to WGA), but it doesn't provide any information as to whether two variants come from the same or different chromosomes as they're usually >1Kb apart and our reads are paired end 76bp (Solexa). For many samples we are unable to get familial DNA so we'd like to directly phase the two SNP in our patients DNA. Does anyone have experience in this area? I've dug through the literate and see that there are a bunch of options (long range PCR, happy mapping, polony, etc); however, none of them appear to be terribly well cited. Which methods did you have the best experience with? Thanks! |
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http://www.chromosomechronicles.com/2009/09/30/use-family-snp-data-to-phase-your-own-genome/ suggests a method for imputing patient phase, when parental microarray data is available. While perhap inaccesible to you today, Complete Genomics sequencing approach returns phased data, and their approach may be useful in your search. |
