10.26091/ESRNZ.9784733.v1
Lisa Melia
Lisa
Melia
Janet Stacey
Janet
Stacey
Rachel Boyle
Rachel
Boyle
Bethany Forsythe
Bethany
Forsythe
A whole mitochondrial genome MPS strategy for low-diversity populations
Institute of Environmental Science and Research
2019
Mitochondrial Gemone
MPS
New Zealand
Pacific Population
Genetic Diversity
Polynesian mitochondrial
mitochondrial DNA
mtDNA
Genetics
2019-09-12 04:12:11
Poster
https://research.esr.cri.nz/articles/poster/A_whole_mitochondrial_genome_MPS_strategy_for_low-diversity_populations/9784733
<p>New Zealand (NZ)
is situated in the South Pacific. The main ethnic groups making up the
population</p>
<p>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.</p>
<p> </p>
<p>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).</p>
<p> </p>
<p>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.</p>