title: HLA-C locus allelic dropout in Sanger sequence-based typing due to intronic single nucleotide polymorphism.
abstract: We report a novel HLA-C allele that was identified during routine HLA typing using sequence-based methods. The patient was initially typed as a C*06:02, 06:04 with two nucleotide mismatches in exon 3, (C to T and T to G changes) which would have resulted in a non-synonymous mutation of a leucine residue being replaced with tryptophan. Further resolution of the patient's type by using sequence-specific primers (SSP) revealed that the companion allele to C*06:02 was a novel C*17:01. Confirmation of the existence of the new allele was performed across multiple platforms: Sanger sequencing, SSP, and Next Generation Sequencing (NGS) on the original sample and allele-specific clones for the entire HLA-C locus. The investigation revealed a single nucleotide mismatch within the Sanger sequencing primer binding site in intron 3. The mutation caused the initial C*17 dropout in exons 2 and 3. Further analysis of the Sanger and NGS data revealed that the C*17 had two additional unique positions in introns 2 and 7. The companion C*06:02 allele also possessed a novel position at intron 3. On August 31, 2013, the WHO nomenclature committee officially named the novel C*17:01 allele sequence as C*17:01:01:03 and the novel C*06:02 allele sequence as C*06:02:01:03.
authors.affiliation: Kashi Clinical Laboratories, Inc., 10101 SW Barbur Blvd., Ste. 200, Portland, OR 97219, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Cheng
authors.affiliation: Kashi Clinical Laboratories, Inc., 10101 SW Barbur Blvd., Ste. 200, Portland, OR 97219, USA.
authors.forename: Zahra Mehdizadeh
authors.initials: ZM
authors.lastname: Kashi
authors.affiliation: Kashi Clinical Laboratories, Inc., 10101 SW Barbur Blvd., Ste. 200, Portland, OR 97219, USA. Electronic address: rmartin@kashilab.com.
authors.forename: Russell
authors.initials: R
authors.lastname: Martin
authors.affiliation: Kashi Clinical Laboratories, Inc., 10101 SW Barbur Blvd., Ste. 200, Portland, OR 97219, USA.
authors.forename: Gillian
authors.initials: G
authors.lastname: Woodruff
authors.affiliation: Life Technologies, Brown Deer, Wisconsin, 9099 N Deerbrook Trail, Brown Deer, WI 53223, USA.
authors.forename: David
authors.initials: D
authors.lastname: Dinauer
authors.affiliation: Life Technologies, Brown Deer, Wisconsin, 9099 N Deerbrook Trail, Brown Deer, WI 53223, USA.
authors.forename: Tina
authors.initials: T
authors.lastname: Agostini
mesh_terms: D001483:Base Sequence; D015236:HLA-C Antigens / Q000235:genetics*; D006650:Histocompatibility Testing; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D015236:HLA-C Antigens; C491620:HLA-C*06:02 antigen; C106777:HLA-C*17:01 antigen
keywords: C*06:02:01:01; C*06:02:01:03; C*17:01:01:02; C*17:01:01:03; HLA-C