- ●A novel microhaplotype (MH) panel containing 188 MHs was developed.
- ●Such panel performed well in multiple evaluations of sequencing quality.
- ●The panel proved satisfactory for 2nd-degree kinship identification.
- ●A new nomenclature of MH loci to eliminate difference among labs was proposed.
- ●Curve fitting to estimate the necessary loci number in distant kinship testing.
Distant kinship identification is one of the critical problems in forensic genetics. As a new type of genetic marker defined and discussed in the last decade, the microhaplotype (MH) has drawn much attention in such identification owing to its specific advantages to traditional short tandem repeat (STR) or single nucleotide polymorphism (SNP) markers. In this study, MH markers were screened step by step from the 1000 Genomes Project database, and a novel multiplex panel containing 188 MHs (in which 181 are reported the first time, while 1 was reported in a previous study and the other 6 have partial overlaps with known markers) was constructed for application in 2nd- and 3rd-degree kinship identification. Along with the construction, a novel MH nomenclature was proposed, in which the SNP position information they contained was taken into account to eliminate the possibility that the same locus was named differently interlaboratory. After a series of evaluations, the panel was shown to have good sequencing accuracy, high sensitivity, species specificity, and resistance to anti-PCR inhibitors or degradation. Population data of the 188 MHs were calculated based on the genetic information of 221 unrelated Hebei Han individuals, and the effective number of alleles (Ae) ranged from 2.0925 to 8.2634 (with an average of 2.9267). For the whole system, the cumulative matching probability (CMP), the cumulative power of exclusion in paternity testing of duos (CPEduo) and that of trios (CPEtrio) reached 2.8422 × 10−137, 1–1.3109 × 10−21, and 1–2.8975 × 10−39, respectively, indicating that this panel was satisfactory for individual identification and paternity testing. Then, the efficiency of the 188 MHs in 2nd- and 3rd-degree kinship testing was studied based on 30 extended families consisting of 179 2nd-degree and 121 3rd-degree relatives, as well as simulations of 0.5 million pairs of those two kinships. The results showed that clear opinions would be given in 83.36% of 2nd-degree identifications with a false rate less than 10−5, when the confirming and excluding thresholds of cumulative likelihood ratio (CLR) were set as 104 and 10−4, respectively. This panel is still not sufficient to solve the problem of 3rd-degree kinship identification alone, and approximately 300 or 870 MH loci would be needed in 2nd- or 3rd-degree kinship identification, respectively, to achieve a system efficiency not less than 0.99 with such a threshold set; such necessary numbers would be used only as a reference in further research.
Abbreviations:MH (microhaplotype), STR (short tandem repeat), SNP (single nucleotide polymorphism), Ae (effective number of alleles), HB (balance of heterozygote), AF (allele frequency matrix), MAF (minimum allele frequency), Hobs (observed heterozygosity), Hexp (expected heterozygosity), MP (matching probability), TDP (total power of discrimination), PIC (polymorphism information content), TPI (typical paternity index), CPEduo (cumulative probability of exclusion for duo paternity testing), CPEtrio (cumulative probability of exclusion for trio paternity testing), HWE (Hardy-Weinberg equilibrium), LD (linkage disequilibrium), CLR (cumulative likelihood ratio), CPI (cumulative paternity index), CFSI (cumulative full-sibling index), ROC curve (receiver operating characteristic curve), AUC (area under the ROC curve), PPV (Positive Predictive Value), NPV (Negative Predictive Value), LOH (loss of heterozygosity), DoC (depth of coverage), MCSA (minor contributor-specific alleles), MRF (minimum allele reads frequency), KS (individual pairs with specific kinship), PO (parent-offspring pair), FS (full-sibling pair), 2ND (2nd-degree relatives), 3RD (3rd-degree relatives), UR (unrelated pairs)
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- Mutation analysis of 28 autosomal short tandem repeats in the Chinese Han population.Mol. Biol. Rep. 2021; 48: 5363-5369
- Mutation rate evaluation at 21 autosomal STR loci: Paternity testing experience.Leg. Med (Tokyo). 2022; 58102080
- A brief review of short tandem repeat mutation.Genom., Proteom. Bioinforma. 2007; 5: 7-14
- Y-chromosomal microsatellite mutation rates: differences in mutation rate between and within loci.Hum. Mutat. 2004; 23: 117-124
- Mutation patterns at dinucleotide microsatellite loci in humans.Am. J. Hum. Genet. 2002; 70: 625-634
- Human genome sequence variation and the influence of gene history, mutation and recombination.Nat. Genet. 2002; 32: 135-142
- Microhaplotype loci are a powerful new type of forensic marker.Forensic Sci. Int.: Genet. Suppl. Ser. 2013; 4: e123-e124
- Pairwise kinship testing with microhaplotypes: can advancements be made in kinship inference with these markers?.Forensic Sci. Int. 2021; 325110875
- A microhap panel for kinship analysis through massively parallel sequencing technology.Electrophoresis. 2019; 41: 246-253
- Evaluation of microhaplotypes in forensic kinship analysis from a Swedish population perspective.Int. J. Leg. Med. 2021;
- Identification of missing persons through kinship analysis by microhaplotype sequencing of single-source DNA and two-person DNA mixtures.Forensic Sci. Int. Genet. 2022; 58102689
- A highly polymorphic panel of 40-plex microhaplotypes for the Chinese Han population and its application in estimating the number of contributors in DNA mixtures.Forensic Sci. Int. Genet. 2022; 56102600
- Identification and sequencing of 59 highly polymorphic microhaplotypes for analysis of DNA mixtures.Int. J. Leg. Med. 2021;
- Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures.Forensic Sci. Int. Genet. 2022; 59102705
- A novel set of short microhaplotypes based on non-binary SNPs for forensic challenging samples.Int. J. Leg. Med. 2021;
- The population genetics characteristics of a 90 locus panel of microhaplotypes.Hum. Genet. 2021;
- Evaluation of three microhaplotypes in individual identification and ancestry inference.Forensic Sci. Int. 2021; 320110681
- Ancestry inference of 96 population samples using microhaplotypes.Int. J. Leg. Med. 2018; 132: 703-711
- Screening and selection of 21 novel microhaplotype markers for ancestry inference in ten Chinese subpopulations.Forensic Sci. Int. Genet. 2022; 58102687
- A 124-plex microhaplotype panel based on next-generation sequencing developed for forensic applications.Sci. Rep. 2020; 10
- Building a custom large-scale panel of novel microhaplotypes for forensic identification using MiSeq and Ion S5 massively parallel sequencing systems.Forensic Sci. Int. Genet. 2020; 45102213
- A sequence-based 74plex microhaplotype assay for analysis of forensic DNA mixtures.Forensic Sci. Int. Genet. 2020; 49102367
- A microhaplotypes panel for forensic genetics using massive parallel sequencing.Forensic Sci. Int.: Genet. Suppl. Ser. 2017; 6: e117-e118
- The International HapMap Project, Nature 426(6968) (2003) 789–96.
- A new statistical method for haplotype reconstruction from population data.Am. J. Hum. Genet. 2001; 68: 978-989
- Criteria for selecting microhaplotypes: mixture detection and deconvolution.Invest. Genet. 2015; 6: 1-10
- fastp: an ultra-fast all-in-one FASTQ preprocessor.Bioinforma. (Oxf., Engl. ). 2018; 34: i884-i890
- Arlequin (version 3.0): an integrated software package for population genetics data analysis.Evol. Bioinform Online. 2007; 1: 47-50
- The derivation of joint distribution and correlation between relatives by the use of stochastic matrices.Biometrics. 1954; 10: 347-360
- MicroHapDB: a portable and extensible database of all published microhaplotype marker and frequency data.Front Genet. 2020; 11: 781
- Development and application of a nonbinary SNP-based microhaplotype panel for paternity testing involving close relatives.Forensic Sci. Int. Genet. 2020; 46102255
- Screening of highly discriminative microhaplotype markers for individual identification and mixture deconvolution in East Asian populations.Forensic Sci. Int Genet. 2022; 59102720
- Proposed nomenclature for microhaplotypes.Hum. Genom. 2016; 10: 16
- A microhaplotypes panel for massively parallel sequencing analysis of DNA mixtures.Forensic Sci. Int. Genet. 2019; 40: 140-149
- Utility of ForenSeq™ DNA signature prep kit in the research of pairwise 2nd-degree kinship identification.Int. J. Leg. Med. 2019; 133: 1641-1650
- Development of an NGS panel containing 42 autosomal STR loci and the evaluation focusing on secondary kinship analysis.Int. J. Leg. Med. 2020; 134: 2005-2014
- Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM.Forensic Sci. Int. Genet. 2015; 17: 110-121
- of next generation sequencing for forensic SNP analysis.Forensic Sci. Int. Genet. 2015; 14: 50-60
- Next generation sequencing of SNPs using the HID-Ion AmpliSeq™ identity panel on the ion torrent PGM™ platform.Forensic Sci. Int. Genet. 2016; 25: 73-84
- Massively parallel sequencing of forensic STRs and SNPs using the Illumina® ForenSeq™ DNA signature prep kit on the MiSeq FGx™ forensic genomics system.Forensic Sci. Int.: Genet. 2017; 31: 135-148
- SNP typing using the HID-Ion AmpliSeq™ identity panel in a southern Chinese population.Int. J. Leg. Med. 2018; 132: 997-1006
- Developmental validation of the MiSeq FGx forensic genomics system for targeted next generation sequencing in forensic DNA casework and database laboratories.Forensic Sci. Int. Genet. 2017; 28: 52-70
- A shortest path-based approach for copy number variation detection from next-generation sequencing data.Front Genet. 2022; 13: 1084974
- Pairwise kinship analysis of 17 pedigrees using massively parallel sequencing.Forensic Sci. Int Genet. 2021; 57102647
- A 472-SNP panel for pairwise kinship testing of second-degree relatives.Forensic Sci. Int. Genet. 2018; 34: 178-185
- Exploring the efficacy of paternity and kinship testing based on single nucleotide polymorphisms.Forensic Sci. Int. Genet. 2016; 22: 161-168
- Robust relationship inference in genome-wide association studies.Bioinforma. (Oxf. Engl.). 2010; 26: 2867-2873
Published online: March 07, 2023
Accepted: March 2, 2023
Received in revised form: February 17, 2023
Received: September 23, 2022
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