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A whole mitochondrial genome MPS strategy for low-diversity populations

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posted on 12.09.2019 by Lisa Melia, Janet Stacey, Rachel Boyle, Bethany Forsythe

New Zealand (NZ) is situated in the South Pacific. The main ethnic groups making up the population

are categorised as self-declared Caucasians (mostly European or Middle Eastern including Iraqis and Iranians), Eastern Polynesians (including NZ Maori, Cook Islanders, Tokelauans, Hawaiians or Tahitians), Western Polynesians (Samoans, Tongans or Niueans) or peoples from Asia (mostly Chinese, Koreans, Japanese, or Filippinos). Genetic diversity within individual Pacific populations is low. About 5500 years ago (ya) Asian migrants from Taiwan became admixed with peoples from New Guinea and Melanesia prior to migration into Western Polynesia ~3000-3500 ya beginning in Fiji which has the highest overall genetic diversity. There is a gradual West-to-East decrease in overall diversity due to founder effects. Polynesian mitochondrial (mt) haplotypes include a 9bp deletion plus three temporally embedded substitutions known as the Polynesian motif. The 9bp intergenic deletion occurred ~60,000ya in Southeast Asia and subsequently three temporally embedded substitutions occurred at nucleotide positions (np) 16217, followed by np16261 ~6000ya in Taiwan and then np16247 in East Indonesia. The motif is now almost fixed in Polynesians. Migration proceeded to Tonga and Samoa ~4200-3000ya, into Eastern Polynesia about 2000-1000ya and finally from Tahiti to NZ via the Cook Islands ~750ya. The haplotype B4a1a1 is fixed in NZ Maori.

Sanger sequencing of the control region of mitochondrial DNA (mtDNA) has not been validated for casework use in NZ due to costs involved in having a purpose-built facility and a labour intensive workflow, together with reduced discrimination for Pacific Island and Maori subpopulations. ESR now has a sequencing facility and with the availability of third party analysis software for forensic applications, we are re-evaluating the costs and discrimination potential of whole genome mitochondrial sequencing using massively parallel sequencing (MPS).

An evaluation was undertaken of a strategy designed to minimise errors from PCR and library preparation chemistries to enable reliable detection of low-level heteroplasmy for reference-type samples, including buccal samples on both Whatman® FTA® card and swabs with the registered mark R after Whatman and after FTA.

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