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http://www.ncbi.nlm.nih.gov/variation/tools/get-rmCallsTestscSRAConcordantDiscordantNATarget audience: Clinical testing labsSubmissions from: Clinical and Research labs
Reporting Standards: Not standardTwelve submitting labs to dateTwelve custom scripts to regularize dataDespite defined formats here:http://www.ncbi.nlm.nih.gov/projects/variation/get-rmWhat are the issues?
Reporting Standards: Not standardWhat are the issues?Better Example: QUAL**Required sixth column in VCF file10.01-18357.112.6-21.20-21.220-3070Allele string34.79-44624.03None20-46006
c.1956+15C>CTReporting Standards: Not standardWhat are the issues?Lab reporting a single nucleotide change (C->T) het change as:c.1956+15C>T[=]HGVS standards says this should be reported as:Lab reporting a single nucleotide change (A->G) hom change as:c.670+9A>GHGVS standards says this should be reported as:c.[670+9A>G];[670+9A>G]
Defining a reference sequence: Data validationNM_007171.3:c.942T>CReported as:Base in transcript is a ‘C’ not a ‘T’
Standardize data: what is the variation?607008.0001985A>G985A>G (K304E)A985GACADM, LYS304GLUK304EK304E (985 A->G)K304E (K329E)K304E onlyK329EK329E(985A>G)LYS304GLUMutation c.985A>G (p.K304E)c.985A>Gc.985A>G (p.K304E)c.985A>G (p.Lys304Gluincludes: K304E (985A>G)p.K304Ep.Lys329Glupreviously known as p.Lys329GluAnalysis of ACADM 985A>G mutationNC_000001.10:g.76226846A>GNG_007045.1:g.41804A>GNM_000016.4:c.985A>GNP_000007.1:p.Lys329Glurs77931234