HLA Twin Workshop EFI 2016 Beginners Answers
INTRODUCTION TO NGS-‐
BASED HLA TYPING WITH HLA
TWIN
ANSWERS FOR RESEARCH USE ONLY
EFI 30th Annual Meeting Omixon Limited
Exercise 1 – HLA Twin Orientation and Analysis of a “Good” Sample Q 1: How large are the fastq files that make up the Good Sample? A 1: 37 MB and 41 MB. Q 2: Which loci is HLA Twin assigning as homozygous? A 2: HLA-‐A and HLA-‐DPB1. Q 3: What region is there a mismatch and what is the nature of the mismatch? A 3: Intron 2, deletion. Q 4: Which loci and QC metrics are flagged with the Info tag? A 4: HLA-‐A, HLA-‐DPB1, HLA-‐DQA1 and HLA-‐DQB1. Q 5: What are the thresholds for read length in the QC metrics? A 5: ≥200 PASSED, 190-‐200 INFO, 150-‐190 INSPECT, ≤150 INVESTIGATE, none FAILED.
Introduction to NGS-‐based HLA Typing with HLA Twin. Copyright© 2016, Omixon Ltd. Confidential & Proprietary
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Exercise 2 – Analysis of a challenging sample Q 1: What is causing the failure flag to get called? (Hint: Go to the Quality Control tab) A 1: Consensus coverage minimum depth is too low (4). Q 2: What is the locus, allele, and exon that is causing the failure flag to get called? (Hint: Use the genome browser for the locus in question) A 2: HLA-‐C*07:02:01:03, exon 3. Q 3: What are the Maximum pairs listed for both of the Challenging Sample analyses? A 3: 4000 and 6000 read pairs. Q 4: What is the minimum depth of coverage for HLA-‐C? (Hint: Use the Quality control tab OR the genome browser at Exon 3) A 4: It is 23.
Introduction to NGS-‐based HLA Typing with HLA Twin. Copyright© 2016, Omixon Ltd. Confidential & Proprietary
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