Highlights
- ●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.
Abstract
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)Keywords
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Article info
Publication history
Published online: March 07, 2023
Accepted:
March 2,
2023
Received in revised form:
February 17,
2023
Received:
September 23,
2022
Identification
Copyright
© 2023 Elsevier B.V. All rights reserved.
