10/26/14
Customer and AccuraScience LB discussed over phone about analysis strategies of a set of targeted resequencing dataset (targeting 12 genes) in a case-control study of a complex disease. AccuraScience LB proposes a plan for Customer to consider.
Thu, 11/27/2014 at 10:48 AM
AccuraScience LB: (Abbreviated version of the proposal) (1) Process targeted resequencing data (focusing on 12 genes) for 190 human samples (including 86 "disease" and 84 "control"), including (a) sequencing data quality control, (b) mapping of all reads to the reference genome, and (c) Perform variant calling (for SNVs and Indels), and present the results in an easily understandable format with detailed base-call count information. (2) Obtain variant calling data for healthy individuals for matching human population (African American) from 1000-genomes project and/or HapMap project. Note: (i) if variant calling information is unavailable, then variant calling will be conducted. (ii) If microarray-based genotyping data (e.g., those from HapMap project) are to be used, then proper treatment (including genotyping imputation) will be conducted to make the data comparable with sequencing-based genotyping results. (3) Predict functional consequences for individual variants called for for each subjects in the "disease", "control", and "general population" groups using multiple tools selected from ANNOVA, SIFT, PolyPhen2, LTR, and MutationTaster, (4) Produce all results in formats specified by Client suitable for further examination and for publication.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
Disclaimer: This text was selected and edited based on genuine communications that took place between a customer and AccuraScience data analysis team at specified dates and times. The editing was made to protect the customer’s privacy and for brevity. The edited text may or may not have been reviewed and approved by the customer. AccuraScience is solely responsible for the accuracy of the information reflected in this text.