Computational protocol: Mitochondrial DNA ancestry, HPV infection and the risk of cervical cancer in a multiethnic population of northeastern Argentina

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Protocol publication

[…] mtDNA haplotypes were defined through direct sequencing of the HVS1 region of the control region (np 16024–16383). Briefly, the HVS1 was PCR amplified using primers 15977-F (5´-CCA CCA TTA GCA CCC AAA GC-3´) and 16552-R (5´-TAA GGG GAA CGT GTG GGC-3´). Positive amplicons were purified using commercial kits (ADN PuriPrep-GP kit, Inbio Highway) and directly sequenced using the original primers through sequencing services using a Beckman Coulter CEQ 2000XL DNA Analysis System (Cromatida, Argentina). A total of 320 samples were processed and 280 were positive for mtDNA (87.5%). Of these, quality sequences were obtained from 261 samples (93.2%). The mtDNA sequences were edited and aligned using Codon Code aligner software v 3.0.1 (CodonCode Corporation). HVS1 haplotypes were classified into haplogroups by using HaploGrep and Phylotree build 17.0 [, ]. mtDNA haplotypes and their haplogroup status are shown in . HVS-1 sequences were deposited in GenBank under accession numbers: KY344532—KY344740. […]

Pipeline specifications

Software tools HaploGrep
Databases nextstrain
Application Phylogenetics
Organisms Homo sapiens, Human papillomavirus type 16, Human papillomavirus
Diseases Brain Diseases, Infection, Neoplasms