A Brief Introduction to Microhaplotypes and their Uses

Main Article Content

Kenneth K. Kidd, Professor Emeritus Daniele Podini, Assoc. Professor and Chair

Abstract

Microhaplotypes are genetic markers that are short DNA sequences, typically consisting of two or more single nucleotide polymorphisms (SNPs) sufficiently close molecularly (<300 basepairs) that their alleles are inherited together from parent to child. Microhaplotypes can be considered a special class of haplotypes, “micro” because they extend for only a few dozens of basepairs, not thousands of basepairs. The advantage of microhaplotypes is that, with massively parallel sequencing of a small segment, the phase is known. Microhaps have been shown to be highly informative in demonstrating uniqueness of DNA profiles and in determining the biogeographic ancestry of an individual. Tests of biologic relationships, such as paternity tests, can be done with microhaplotypes. Deconvolution of DNA mixtures is an area in which microhaplotypes appear to be especially promising. This brief introductory review presents the scientific background for the development of microhaplotypes as a new type of genetic marker and examples of some of the recent applications.

Article Details

How to Cite
KIDD, Kenneth K.; PODINI, Daniele. A Brief Introduction to Microhaplotypes and their Uses. Medical Research Archives, [S.l.], v. 12, n. 3, mar. 2024. ISSN 2375-1924. Available at: <https://esmed.org/MRA/mra/article/view/5142>. Date accessed: 30 apr. 2024. doi: https://doi.org/10.18103/mra.v12i3.5142.
Section
Research Articles

References

1. Kidd KK, Pakstis AJ, Speed WC, Lagace R, Chang J, Wootton S, Ihuegbu N.. Microhaplotype loci are a powerful new type of forensic marker. Forensic Sci Int Genet Suppl Ser. 2013; 4:e123-e124.
2. Kidd KK, Pakstis AJ, Speed WC, Lagace R, Chang J, Wootton S, E. Haigh, J.R. Kidd. Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics. Forensic Sci Int Genet. 2014 Sep; 12:215-24. Doi:10.1016/j.fsigen.2014.06.014. Epub 2014 Jul 1.
3. Oldoni F, Kidd KK, Podini D. Microhaplotypes in forensic genetics. Forensic Sci Int Genet. 2019; Jan; 38:54-69.
Doi: 10.1016/j.fsigen.2018.09.009. Epub 2018 Oct 1
4. Bodmer W. Ruggero Ceppellini: A perspective on his contributions to genetics and immunology. Front Immunol. 2019; 10:1280. Doi:10.3389/fimmu.2019.01280
5. Hawley ME, Kidd KK.. HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered. 1995 Sep-Oct;86(5):409-411.
Doi: 10.1093/oxfordjournals.jhered.a111613.
6. Stephens M, Smith N, Donnelly P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001; 68:978-989. https://doi.org/10.1086/319501
7. Han Y, Gu S, Oota H, Osier MV, Pakstis AJ, Speed WC, Kidd JR, Kidd KK. Evidence of positive selection on a Class I ADH locus. Am J Hum Genet. 2007 Mar;80(3):441-56. Doi: 10.1086/512485. Epub 2007 Jan 30.
8. Li H, Gu S, Cai X, Speed WC, Pakstis AJ, Golub EI, Kidd JR, Kidd KK. Ethnic Related Selection for an ADH Class I Variant within East Asia. PLoS ONE 2008; 3(4):e1881.
Doi: 10.1371/journal.pone.000188
9. Gu S, Li H, Pakstis AJ, Speed WC, Gurwitz D, Kidd JR, Kidd KK. Recent selection on a Class I ADH locus distinguishes southwest Asian populations including Ashkenazi Jews. Genes 2018; 9: 452 Doi:10.3390/genes9090452
10. Tucker T, Marra, M, Friedman JM. Massively parallel sequencing: The next big thing in genetic medicine. Am J Hum Genet 2009; 85(2):142–154.
Doi: 10.1016/j.ajhg.2009.06.022
11. The 1000 Genomes Project Consortium.. A global reference for human genetic variation. Nature 2015; 526: 68–74 https://doi.org/10.1038/nature15393
12. Kidd KK and Pakstis AJ. State of the art for microhaplotypes. Genes (Basel) 2022; 13(8):1322. Doi: 10.3390/genes13081322.
13. Chen P, Deng C, Li Z, Pu Y, Yang J, Yu Y, Li K, Li D, Liang W, Zhang L, Chen F.. A microhaplotypes panel for massively parallel sequencing analysis of DNA mixtures. Forensic Sci Int Genet. 2019 May;40:140-149.
Doi: 10.1016/j.fsigen.2019.02.018.
14. Liu J, Su Y, Wen Y, Jiang L, Li S, Zhao M, Chen X, Wang Z.. Massively parallel sequencing of 74 microhaplotypes and forensic characteristics in three Chinese Sino-Tibetan populations. Forensic Sci Int Genet. 2023 Sep;66:102905. Doi: 10.1016/j.fsigen.2023.102905.
15. Sun S, Liu Y, Li J, Yang Z, Wen D, Liang W, Yan Y, Yu H, Cai J, Zha L.. Development and application of a nonbinary SNP-based microhaplotype panel for paternity testing involving close relatives. Forensic Sci Int Genet. 2020 May;46:102255.
Doi: 10.1016/j.fsigen.2020.102255.
16. Osborne MJ, Caeiro-Dias G, Turner TF. Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years. Mol Ecol. 2023 Jan;32(2):316-334. Doi: 10.1111/mec.16760.
17. Horne JB, Frey A, Gaos AR, Martin S, Dutton PH. Non-random mating within an island rookery of Hawaiian hawksbill turtles: demographic discontinuity at a small coastline scale. R Soc Open Sci. 2023;10(5):221547.
Doi: 10.1098/rsos.221547.
18. Tessema SK, Hathaway NJ, Teyssier NB, Murphy M, Chen A, Aydemir O, Duarte EM, Simone W, Colborn J, Saute F, Crawford E, Aide P, Bailey JA, Greenhouse B.. Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome. J Infect Dis. 2022 Apr 1;225(7):1227-1237. Doi: 10.1093/infdis/jiaa527.
19. Kidd KK, Pakstis AJ, Gandotra N, Scharfe C, Podini D. A multipurpose panel of microhaplotypes for use with STR markers in casework. Forensic Sci Int Genet. 2022 Sep; 60:102729.
Doi: 10.1016/j.fsigen.2022.102729. Epub 2022 Jun 3.
20. Kidd KK and Speed WC. Criteria for selecting microhaplotypes: mixtures and deconvolution. Investig Genet. 2015 Jan 28; 6:1. Doi:10.1186/s13323-014-0018-3.
21. Budowle B, Moretti TR, Niezgoda SJ, and Brown BL. CODIS and PCR-based short tandem repeat loci: law enforcement tools. Publication number 98-06 of the Laboratory Division of the Federal Bureau of Investigation
22. Gandotra N, Speed WC, Qin W, Tang Y, Pakstis AJ, Kidd KK, Scharfe C. Validation of novel forensic DNA markers using multiplex microhaplotype sequencing. Forensic Sci Int Genet. 2020 Jul; 47:102275. Doi:10.1016/j.fsigen.2020.102275. Epub 2020 Mar 18.
23. Pakstis AJ, Gandotra N, Speed WC, Murtha M, Scharfe C, Kidd KK. 2021. The population genetics characteristics of a 90 locus panel of microhaplotypes. Hum Genet. 2021 Dec;140(12):1753-1773.
Doi: 10.1007/s00439-021-02382-0. Epub 2021 Oct 13.
24. Kan YW, Dozy AM. Antenatal diagnosis of sickle-cell anaemia by D.N.A. analysis of amniotic-fluid cells. Lancet 1978 Oct 28;2(8096):910-2. Doi: 10.1016/s0140-6736(78)91629-x.
25. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics, 2000; 155 (2):945–59 https://doi.org/10.1093/genetics/155.2.945
26. Soundararajan U, Yun L, Shi M, Kidd KK. Minimal SNP overlap among multiple panels of ancestry informative markers argues for more international collaboration. Forensic Sci Int Genet. 2016 Jul;23:25-32. Doi:10.1016/j.fsigen.2016.01.013. Epub 2016 Jan 22.
27. Xue J, Qu S, Tan M, Xiao Y, Zhang R, Chen D, Lv M, Zhang Y, Zhang L, Liang W. An overview of SNP-SNP microhaplotypes in the 26 populations of the 1000 Genomes Project. Int J Legal Med. 2022 Sep;136(5):1211-1226.
Doi: 10.1007/s00414-022-02820-2. Epub 2022 Apr 9.
28. Bulbul O, Pakstis AJ, Soundararajan U, Gurkan G, Brissenden JE, Roscoe JM, Evsanaa B, Togtokh A, Paschou P, Grigorenko EL, Gurwitz D, Wootton S, Lagace R, Chang J, Speed WC, Kidd KK,. Ancestry inference of 96 population samples using microhaplotypes. Int J Legal Med. 2018 May;132(3):703-711. Doi:10.1007/s00414-017-1748-6. Epub 2017 Dec 16.
29. Kidd KK, Evsanaa B, Togtokh A, Brissenden JE, Roscoe JM, Dogan M, Neophytou PI, Gurkan C, Bulbul O, Cherni L, Speed WC, Murtha M, Kidd JR, Pakstis AJ. North Asian population relationships in a global context. Sci Rep. 2022 May 4;12(1):7214. Doi: 10.1038/s41598-022-10706-x.
30. Wu R, Chen H, Li R, Zang Y, Shen X, Hao B, Wang Q, Sun H. Pairwise kinship testing with microhaplotypes: Can advancements be made in kinship inference with these markers? Forensic Sci Int Genet. 2021 Aug;325:110875. Doi: 10.1016/j.forsciint.2021.110875. Epub 2021 Jun 12.
31. Bai Z, Zhao H, Lin S, Huang L, He Z, Wang H, Ou X. Evaluation of a microhaplotype-based noninvasive prenatal test in twin gestations: determination of paternity, zygosity, and fetal fraction. Genes (Basel). 2020 Dec 27;12(1):26. Doi: 10.3390/genes12010026.
32. Qu N, Lin S, Gao Y, Liang H, Zhao H, Ou X. A microhap panel for kinship analysis through massively parallel sequencing technology. Electrophoresis. 2020 Feb;41(3-4):246-253. Doi: https://pubmed.ncbi.nlm.nih.gov/29536546/10.1002/elps.201900337. Epub 2019 Dec 19.
33. Xue J, Tan M, Zhang R, Chen D, Liu G, Zheng Y, Wu Q, Xiao Y, Liao M, Qu S, Liang W. Evaluation of microhaplotype panels for complex kinship analysis using massively parallel sequencing. Forensic Sci Int Genet. 2023 Jul;65:102887..Doi:10.1016/j.fsigen.2023.102887. Epub 2023 May 3.
34. Tang X, Wen D, Wang CD, Xu RY, Jia HT, Li JN, Zhalaga BY. Application of microhaplotypes in sibling kinship testing. J Forensic Med. 2023 Jun 25;39(3):288-295. English, Chinese. Doi: 10.12116/j.issn.1004-5619.2023.530101.
35. Bai Z, Zhang N, Liu J, Ding H, Zhang Y, Wang T, Gao J, Ou X. Identification of missing persons through kinship analysis by microhaplotype sequencing of single-source DNA and two-person DNA mixtures. Forensic Sci Int Genet. 2022 May;58:102689.
Doi: 10.1016/j.fsigen.2022.102689. Epub 2022 Mar 16.
36. Zhu Q, Wang H, Cao Y, Huang Y, Wei Y, Hu Y, Dai X, Shan T, Wang Y, Zhang J. Evaluation of large-scale highly polymorphic microhaplotypes in complex DNA mixtures analysis using RMNE method. Forensic Sci Int Genet. 2023 Jul;65:102874.
Doi: 10.1016/j.fsigen.2023.102874. Epub 2023 Apr 14.
37. Bennett L, Oldoni F, Long K, Cisana S, Madella K, Wootton S, Chang J, Hasegawa R, Lagacé R, Kidd KK, Podini D. Mixture deconvolution by massively parallel sequencing of microhaplotypes. Int J Legal Med. 2019 May;133(3):719-729. Doi: 10.1007/s00414-019-02010-7. Epub 2019 Feb 13.
38. Yu WS, Feng YS, Kang KL, Zhang C, Ji AQ, Ye J, Wang L. Screening of highly discriminative microhaplotype markers for individual identification and mixture deconvolution in East Asian populations. Forensic Sci Int Genet. 2022 Jul;59:102720.
Doi: 10.1016/j.fsigen.2022.102720. Epub 2022 May 15..
39. Oldoni F, Bader D, Fantinato C, Wootton SC, Lagacé R, Kidd KK, Podini D. A sequence-based 74plex microhaplotype assay for analysis of forensic DNA mixtures. Forensic Sci Int Genet. 2020 Nov; 49:102367. Doi:10.1016/j.fsigen.2020.102367.
Epub 2020 Aug 11.