124
Views
1
CrossRef citations to date
0
Altmetric
Research Papers

Forensic evaluation of mitochondrial DNA heteroplasmy in Gujarat population, India

, &
Pages 332-341 | Received 24 May 2022, Accepted 03 Oct 2022, Published online: 18 Nov 2022

References

  • Alonso A, Salas A, Albarrán C, Arroyo E, Castro A, Crespillo M, Di Lonardo AM, et al. 2002. Results of the 1999-2000 collaborative exercise and proficiency testing program on mitochondrial DNA of the GEP-ISFG: an inter-laboratory study of the observed variability in the heteroplasmy level of hair from the same donor. Forensic Sci Int. 125(1):1–7.
  • Amorim A, Fernandes T, Taveira N. 2019. Mitochondrial DNA in human identification: a review. PeerJ. 7:e7314.
  • Anderson S, Bankier AT, Barrell BG, De Bruijn MHL, Coulson AR, Drouin J, Eperon IC, et al. 1981. Sequence and organization of the human mitochondrial genome. Nature. 290(5806):457–465.
  • Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. 1999. Reanalysis and revision of the Cambridge Reference Sequence for human mitochondrial DNA. Nat Genet. 23(2):147.
  • Asari M, Azumi J, Ichi Shimizu K, Shiono H. 2008. Differences in tissue distribution of HV2 length heteroplasmy in mitochondrial DNA between mothers and children. Forensic Sci Int. 175(2–3):155–159.
  • Bandelt HJ, Kloss-Brandstätter A, Richards MB, Yao YG, Logan I. 2014. The case for the continuing use of the revised Cambridge Reference Sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies. J Hum Genet. 59(2):66–77.
  • Barshad G, Marom S, Cohen T, Mishmar D. 2018. Mitochondrial DNA transcription and its regulation: an evolutionary perspective. Trends Genet. 34(9):682–692.
  • Bell JR. 2008. A simple way to treat PCR products prior to sequencing using ExoSAP-IT®. Biotechniques. 44(6):834.
  • Bendall KE, Macaulay VA, Sykes BC. 1997. Variable levels of a heteroplasmic point mutation in individual hair roots. Am J Hum Genet. 61(6):1303–1308.
  • Bendall KE, Sykes BC. 1995. Length heteroplasmy in the first hypervariable segment of the human mtDNA control region. Am J Hum Genet. 57(2):248–256.
  • Brandstätter A, Niederstätter H, Parson W. 2004. Monitoring the inheritance of heteroplasmy by computer-assisted detection of mixed basecalls in the entire human mitochondrial DNA control region. Int J Legal Med. 118(1):47–54.
  • Brown JR, Beckenbach AT, Smith MJ. 1993. Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus). Mol Biol Evol. 10(2):326–341.
  • Brown WM, Prager EM, Wang A, Wilson AC. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol. 18(4):225–239.
  • Budowle B, Allard MW, Wilson MR, Chakraborty R. 2003. Forensics and Mitochondrial DNA: applications, Debates, and Foundations. Annu Rev Genomics Hum Genet. 4:119–141.
  • Calloway CD, Reynolds RL, Herrin GL, Anderson WW. 2000. The frequency of heteroplasmy in the HVII region of mtDNA differs across tissue types and increases with age. Am J Hum Genet. 66(4):1384–1397.
  • Cavelier L, Jazin E, Jalonen P, Gyllensten U. 2000. MtDNA substitution rate and segregation of heteroplasmy in coding and noncoding regions. Hum Genet. 107(1):45–50.
  • Cui H, Li F, Chen D, Wang G, Truong CK, Enns GM, Graham B, et al. 2013. Comprehensive next-generation sequence analyses of the entire mitochondrial genome reveal new insights into the molecular diagnosis of mitochondrial DNA disorders. Genet Med. 15(5):388–394.
  • Duan M, Tu J, Lu Z. 2018. Recent advances in detecting mitochondrial DNA heteroplasmic variations. Molecules. 23(2):323–18.
  • Egeland T, Salas A. 2011. A statistical framework for the interpretation of mtDNA mixtures: forensic and medical applications. PLOS One. 6(10):e26723.
  • Fazzini F, Schöpf B, Blatzer M, Coassin S, Hicks AA, Kronenberg F, Fendt L. 2018. Plasmid-normalized quantification of relative mitochondrial DNA copy number. Sci Rep. 8(1):11.
  • Fernández-Silva P, Enriquez JA, Montoya J. 2003. Replication and transcription of mammalian mitochondrial DNA. Exp Physiol. 88(1):41–56.
  • Gill P, Ivanov PL, Kimpton C, Piercy R, Benson N, Tully G, Evett I, et al. 1994. Identification of the remains of the Romanov family by DNA analysis. Nat Genet. 6(2):130–135
  • González AM, Larruga JM, Abu-Amero KK, Shi Y, Pestano J, Cabrera VM. 2007. Mitochondrial lineage M1 traces an early human backflow to Africa. BMC Genomics. 8:223–12.
  • Greenberg BD, Newbold JE, Sugino A. 1983. Intraspecific nucleotide sequence variability surrounding the origin of replication in human mitochondrial DNA. Gene. 21(1–2):33–49.
  • Hallmaier-Wacker LK, Lueert S, Roos C, Knauf S. 2018. The impact of storage buffer, DNA extraction method, and polymerase on microbial analysis. Sci Rep. 8(1):9.
  • Hauswirth WW, Van De Walle MJ, Laipis PJ, Olivo PD. 1984. Heterogeneous mitochondrial DNA D-loop sequences in bovine tissue. Cell. 37(3):1001–1007.
  • Heyer E, Zietkiewicz E, Rochowski A, Yotova V, Puymirat J, Labuda D. 2001. Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees. Am J Hum Genet. 69(5):1113–1126.
  • Holland MM, Parsons TJ. 1999. Mitochondrial DNA sequence analysis – validation and use for forensic casework. Forensic Sci Rev. 11(1):21–50.
  • Ingman M, Gyllensten U. 2003. Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Res. 13(7):1600–1606.
  • Irwin JA, Saunier JL, Niederstätter H, Strouss KM, Sturk KA, Diegoli TM, Brandstätter A, et al. 2009. Investigation of heteroplasmy in the human mitochondrial DNA control region: a synthesis of observations from more than 5000 global population samples. J Mol Evol. 68(5):516–527.
  • Ivanov PL, Wadhams MJ, Roby RK, Holland MM, Weedn VW, Parsons TJ. 1996. Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II. Nat Genet. 12(4):417–420.
  • Kivisild T, Kaldma K, Metspalu M, Parik J, Papiha S, Villems R. 1999. The place of the Indian mitochondrial DNA variants in the global network of maternal lineages and the peopling of the old world. In: Papiha SS, Deka R, Chakraborty, R, editors. Genomic diversity. Boston (MA): Springer; p. 135–152.
  • Lee HY, Chung U, Yoo JE, Park MJ, Shin KJ. 2004. Quantitative and qualitative profiling of mitochondrial DNA length heteroplasmy. Electrophoresis. 25(1):28–34.
  • Lee C, Măndoiu II, Nelson CE. 2011. Inferring ethnicity from mitochondrial DNA sequence. BMC Proc. 5(S2):S11.
  • Lee SD, Shin CH, Kim KB, Lee YS, Lee JB. 1997. Forensic Science International Sequence variation of mitochondrial DNA control region in Koreans. Forensic Sci Int. 87(2):99–116.
  • Lee JCI, Tsai LC, Yu YJ, Lin CY, Linacre A, Hsieh HM. 2016. Investigation into length heteroplasmy in the mitochondrial DNA control region after treatment with bisulfite. J Formos Med Assoc. 115(4):284–287.
  • Li M, Rothwell R, Vermaat M, Wachsmuth M, Schröder R, Laros JFJ, Van Oven M, Genome of Netherlands Consortium, et al. 2016. Transmission of human mtDNA heteroplasmy in the genome of the Netherlands families: support for a variable-size bottleneck. Genome Res. 26(4):417–426.
  • Li M, Schröder R, Ni S, Madea B, Stoneking M. 2015. Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations. Proc Natl Acad Sci USA. 112(8):2491–2496.
  • Lutz-Bonengel S, Sänger T, Parson W, Müller H, Ellwart JW, Follo M, Bonengel B, et al. 2008. Single lymphocytes from two healthy individuals with mitochondrial point heteroplasmy are mainly homoplasmic. Int J Legal Med. 122(3):189–197.
  • Lutz S, Weisser HJ, Heizmann J, Pollak S. 1998. Location and frequency of polymorphic positions in the mtDNA control region of individuals from Germany. Int J Legal Med. 111(2):67–77.
  • Lutz S, Weisser HJ, Heizmann J, Pollak S. 2000. Mitochondrial heteroplasmy among maternally related individuals. Int J Legal Med. 113(3):155–161.
  • Mabuchi T, Susukida R, Kido A, Oya M. 2007. Typing the 1.1 kb control region of human mitochondrial DNA in Japanese individuals. J Forensic Sci. 52(2):355–363.
  • Maji S, Krithika S, Vasulu TS. 2008. Distribution of mitochondrial DNA macrohaplogroup N in India with special reference to haplogroup R and its sub-haplogroup U. Int. J. Hum. Genet. 8(1–2):85–96.
  • Malik S, Sudoyo H, Pramoonjago P, Suryadi H, Sukarna T, Njunting M, Sahiratmadja E, Marzuki S. 2002. Nuclear mitochondrial interplay in the modulation of the homopolymeric tract length heteroplasmy in the control (D-loop) region of the mitochondrial DNA. Hum Genet. 110(5):402–411.
  • Melton T. 2004. Mitochondrial DNA heteroplasmy. Forensic Sci Rev. 16(1):1–20.
  • Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, Kaldma K, Serk P, et al. 2004. Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genet. 5:26–25.
  • Mitchell SL, Goodloe R, Brown-Gentry K, Pendergrass SA, Murdock DG, Crawford DC. 2014. Characterization of mitochondrial haplogroups in a large population-based sample from the United States. Hum Genet. 133(7):861–868.
  • Naue J, Hörer S, Sänger T, Strobl C, Hatzer-Grubwieser P, Parson W, Lutz-Bonengel S. 2015. Evidence for frequent and tissue-specific sequence heteroplasmy in human mitochondrial DNA. Mitochondrion. 20:82–94.
  • Nilsson M. 2007. Mitochondrial DNA in sensitive forensic analysis [dissertation]. Uppsala:Uppsala University.
  • Parson W, Bandelt HJ. 2007. Extended guidelines for mtDNA typing of population data in forensic science. Forensic Sci Int Genet. 1(1):13–19.
  • Parson W, Dür A. 2007. EMPOP—a forensic mtDNA database. Forensic Sci Int Genet. 1(2):88–92.
  • Parson W, Gusmão L, Hares DR, Irwin JA, Mayr WR, Morling N, Pokorak E, DNA Commission of the International Society for Forensic Genetics, et al. 2014. DNA Commission of the International Society for Forensic Genetics: revised and extended guidelines for mitochondrial DNA typing. Forensic Sci Int Genet. 13:134–142.
  • Passarino G, Semino O, Bernini LF, Santachiara-Benerecetti AS. 1996. Pre-caucasoid and caucasoid genetic features of the Indian population, revealed by mtDNA polymorphisms. Am J Hum Genet. 59(4):927–934.
  • Poulton J, Brown MS, Cooper A, Marchington DR, Phillips DI. 1998. A common mitochondrial DNA variant is associated with insulin resistance in adult life. Diabetologia. 41(1):54–58.
  • Rajkumar R, Banerjee J, Gunturi HB, Trivedi R, Kashyap VK. 2005. Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages. BMC Evol Biol. 5(1):26.
  • Rasmussen E, Sørensen E, Eriksen B, Larsen H, Morling N. 2002. Sequencing strategy of mitochondrial HV1 and HV2 DNA with length heteroplasmy. Forensic Sci Int. 129(3):209–213.
  • Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sanchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 34(12):3299–3302.
  • Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC. 2004. Effects of purifying and adaptive selection on regional variation in human mtDNA. Science. 303(5655):223–226.
  • Salas A, Carracedo Á, Macaulay V, Richards M, Bandelt HJ. 2005. A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. Biochem Biophys Res Commun. 335(3):891–899.
  • Salas A, Lareu MV, Carracedo A. 2001. Heteroplasmy in mtDNA and the weight of evidence in forensic mtDNA analysis: a case report. Int J Legal Med. 114(3):186–190.
  • Samuels DC, Li C, Li B, Song Z, Torstenson E, Boyd Clay H, Rokas A, et al. 2013. Recurrent tissue-specific mtDNA mutations are common in humans. PLOS Genet. 9(11):e1003929.
  • Sanchez-Cespedes M, Parrella P, Nomoto S, Cohen D, Xiao Y, Esteller M, Jeronimo C, et al. 2001. Identification of a mononucleotide repeat as a major target for mitochondrial DNA alterations in human tumors. Cancer Res. 61(19):7015–7019.
  • Santos C, Montiel R, Sierra B, Bettencourt C, Fernandez E, Alvarez L, Lima M, et al. 2005. Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores Islands (Portugal). Mol Biol Evol. 22(6):1490–1505.
  • Santos C, Sierra B, Álvarez L, Ramos A, Fernández E, Nogués R, Aluja MP. 2008. Frequency and pattern of heteroplasmy in the control region of human mitochondrial DNA. J Mol Evol. 67(2):191–200.
  • Thangaraj K, Chaubey G, Singh VK, Vanniarajan A, Thanseem I, Reddy AG, Singh L. 2006. In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup “M” in India. BMC Genomics. 7:151.
  • Tikochinski Y, Carreras C, Tikochinski G, Vilaça ST. 2020. Population-specific signatures of intra-individual mitochondrial DNA heteroplasmy and their potential evolutionary advantages. Sci Rep. 10(1):14.
  • van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat. 30(2):E386–E394.
  • Vanecek T, Vorel F, Sip M. 2004. Mitochondrial DNA D-loop hypervariable regions: Czech population data. Int J Legal Med. 118(1):14–18.
  • Vaught JB. 2006. Blood collection, shipment, processing, and storage. Cancer Epidemiol Biomarkers Prev. 15(9):1582–1584.
  • Wallace DC. 1994. Mitochondrial DNA sequence variation in human evolution and disease. Proc Natl Acad Sci USA. 91(19):8739–8746.
  • Wallace DC, Chalkia D. 2013. Mitochondrial DNA genetics and the heteroplasmy conundrum in evolution and disease. Cold Spring Harb. Perspect. Med. 5(11):a021220–a021220.
  • Wallace DC, Ye J, Neckelmann SN, Singh G, Webster KA, Greenberg BD. 1987. Sequence analysis of cDNAs for the human and bovine ATP synthase β subunit: mitochondrial DNA genes sustain seventeen times more mutations. Curr Genet. 12(2):81–90.
  • Wells RS, Behar DM, Sayar H, Scozzari R, Rengo C, Al-Zahery N, Semino O, et al. 2004. Where West Meets East: the complex mtDNA landscape of the southwest and Central Asian corridor. Am J Hum Genet. 74(5):827–845.
  • White DJ, Wolff JN, Pierson M, Gemmell NJ. 2008. Revealing the hidden complexities of mtDNA inheritance. Mol Ecol. 17(23):4925–4942.
  • Wilkinson-Herbots HM, Richards MB, Forster P, Sykes BC. 1996. Site 73 in hypervariable region II of the human mitochondrial genome and the origin of European populations. Ann Hum Genet. 60(6):499–508.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.