Journal List > Korean J Leg Med > v.37(4) > 1004719

Cho, Yu, Han, Lee, Lee, and Lee: Genetic Relationship in Bone Samples Using SNP-Based Human Identification DNA Chip

Abstract

DNA profiling with sets of short tandem repeat (STR) markers is the most popular method for identifying human DNA in forensics. Identification by STR typing might fail when DNA is degraded or is present in low amounts, such as in disaster victim identification (DVI) samples. In such cases, more information might be obtained by using additional markers such as single nucleotide polymorphisms (SNPs). Multiplex PCR and microarray are convenient techniques to analyze SNP markers. We used an AccuID Chip, SNP-based DNA chip manufactured by DNA Link Corporation, to confirm genetic relationship between two human bone samples that had been buried for more than 50 years and blood samples from the alleged descendants of the sources of the bone fragments. The chip combines an Affymetrix resequencing array with a multiplex PCR technology and can genotype hundreds of SNP markers in a single experiment. Genotyping the two bone samples yielded 90.5 and 77 SNP markers. The commonly genotyped markers (61 and 47 SNP loci) in each bone-family pair provided high paternity indices to support the genetic relationships in both cases.

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Fig. 1.
Sequencing array design. Eight 25-mers are tiled to probe each individual base pair. A single position differs so that each of the four possible nucleotides can be queried on both the sense and antisense strands (a, adapted from reference 4). The probe designed in triplicate provides advantages in the aspect of accuracy, confidence, and reproducibility (b, illustrated by Hyung Jin Yu, DNA Link).
kjlm-37-224f1.tif
Table 1.
The Average Minor Allele Frequency (MAF) and Fixation Index (Fst) Value of 169 Markers
Chromosome Number of markers Average MAF Average Fst
1 11 0.474 0.01
2 15 0.467 0.011
3 10 0.464 0.012
4 12 0.47 0.014
5 14 0.464 0.012
6 17 0.476 0.009
7 8 0.477 0.015
8 11 0.457 0.013
9 8 0.455 0.014
10 1 0.458 0.035
11 12 0.461 0.01
12 6 0.477 0.009
13 11 0.469 0.015
14 6 0.452 0.013
15 6 0.461 0.01
16 3 0.472 0.005
17 2 0.404 0.02
18 8 0.462 0.013
19 1 0.415 0.023
20 5 0.472 0.01
21 - - -
22 2 0.412 0.018
Total 169 0.465 0.013
Table 2.
The Result of SNP Typing Using AccuID
Family 1 Bone 1 Family 2 Bone 2
Typed SNP 154   150   87   94 157   152   75   79
        61             47      
Untyped SNP 15   19   82   75 12   17   94   90
    6       60     9       67  
Total SNP 169   169   169   169 169   169   169   169

The number of common SNP markers typed in both blood sample from a family member and bone sample.

The number of common SNP markers which were not typed repeatedly.

Table 3.
The Result of 169 SNP Typing in all Samples
SNP Family 1 Bone 1 Family 2 Bone 2
rs10043269 - - CC CT
rs10055677 - - - -
rs1027636 AG AG AG AG
rs10448261 GG AG - -
rs10455344 - - - -
rs10477259 - - - -
rs10495682 - - CC CT
rs10502033 - - - -
rs10784009 - - AG AG
rs10795736 - - - -
rs10811474 - - - -
rs10851458 AA AG - -
rs10894244 CC AC CC CC
rs10916409 - - - -
rs10926595 - - - -
rs10948570 AG GG AA AG
rs11133959 - - - -
rs11208131 - - - -
rs1150461 - - - -
rs11634785 AG AG - -
rs11648974 - - - -
rs11689668 - - GG GG
rs11784117 AG AG AG AG
rs11887855 - - TT TT
rs11984683 CC AC AC AA
rs2203030 - - - -
rs2241225 CC CT CC CT
rs2270086 - - - -
rs2336695 AG AA - -
rs2391467 - - - -
rs2408032 - - - -
rs241405 - - - -
rs2425427 CT CT - -
rs2613019 CC CC - -
rs2685441 CT TT - -
rs2736966 - - - -
rs2817438 - - CT CT
rs297013 - - - -
rs31042 - - - -
rs3104999 - - - -
rs343835 TT GT - -
rs3761161 GG AG - -
rs397311 - - - -
rs4027132 AA AG AG AG
rs409492 GG GG AG GG
rs4130306 - - - -
rs4427846 - - AG GG
rs4605480 - - - -
rs465530 - - - -
rs4667489 - - - -
rs1211780 TT GT GG GG
rs12135862 - - - -
rs12286769 TT TT - -
rs12443018 - - - -
rs12534955 CT CT CT CT
rs12585235 CT CT CT CT
rs12607426 GG AG AA AA
rs1265216 TT CT CT CT
rs12672158 AG AG - -
rs12695977 - - AG AG
rs12876644 - - - -
rs1290018 - - - -
rs12965342 - - - -
rs13033921 - - CT CT
rs13087528 - - - -
rs13206934 TT CT - -
rs1321167 - - - -
rs13260204 - - - -
rs13265571 - - - -
rs13402508 - - AG AG
rs1340562 AC AC - -
rs1345724 - - - -
rs1350191 - - - -
rs1354147 - - - -
rs1434369 GT GT GT GG
rs4669155 - - - -
rs4671787 - - - -
rs4695907 - - - -
rs4709819 - - - -
rs4834604 - - - -
rs4907923 TT CT CC CC
rs4965786 AG AG - -
rs5010755 - - - -
rs536568 - - AA AC
rs543840 - - - -
rs547041 - - - -
rs581488 - - - -
rs6106856 AG GG AG GG
rs622671 CC CC - -
rs6415441 AA AG AG GG
rs6496145 - - - -
rs6596805 - - AG GG
rs6711114 - - AA AG
rs673745 - - - -
rs6785504 - - - -
rs6799770 - - GG GG
rs6817563 - - - -
rs6819372 AA AA GG GG
rs6840524 AC AA - -
rs6888825 - - - -
rs1440869 - - - -
rs1463965 - - - -
rs1473604 CC AC CC AC
rs1488902 CT CT - -
rs1495816 - - - -
rs1529590 - - - -
rs1539525 AG AG - -
rs1546833 - - - -
rs1563172 - - - -
rs17050202 GG AG GG GG
rs17056706 - - - -
rs1709915 - - - -
rs17103286 GG AG AG GG
rs17111166 AA AG - -
rs1873873 CC CC CT CT
rs1892522 - - - -
rs1897725 CC CC CC CT
rs1942399 - - - -
rs1943338 - - CC CT
rs1998033 CC CC CT CT
rs1998041 - - - -
rs2022958 GT GT - -
rs2039623 - - - -
rs2127657 AG AG AG AG
rs2199479 - - - -
rs6900780 - - - -
rs7027501 - - - -
rs7031829 - - - -
rs7110588 AG AG - -
rs7123330 - - - -
rs7160372 - - - -
rs726432 - - - -
rs7288176 CC CT - -
rs7294966 AG GG - -
rs7300188 TT CT - -
rs7302091 CC CT - -
rs7307697 AA AG AG AG
rs7327729 - - GT GT
rs7337382 AG AG - -
rs7403602 - - - -
rs7441242 GG AG - -
rs7516525 - - - -
rs7579747 GG AG AA AG
rs7664664 - - AG AG
rs769556 - - - -
rs7733022 AG AG - -
rs7749777 - - - -
rs7814747 - - - -
rs7816405 - - CT CC
rs7938115 - - - -
rs8066522 - - - -
rs914532 - - - -
rs9314663 - - - -
rs9364063 - - - -
rs9373570 - - - -
rs9407764 - - - -
rs9496500 AA AA - -
rs950226 AG AG AA AG
rs9530931 - - - -
rs955077 CT CC - -
rs9595960 - - - -
rs9598504 - - - -
rs960513 TT CT - -
rs970022 CT CT CT CC
rs9849464 - - - -
rs990633 - - - -
rs990815 - - - -
rs9940346 - - - -
rs9949516 AA AA - -
Table 4.
The Result of SNP Markers Typed in Bone Samples which are not Identical in Duplicate
SNP Family 1 Bone 1 SNP Family 2 Bone 2
rs10495682 CC CC CT rs13206934 CT TT CT
rs1892522 - GG AG rs2425427 CT CC CT
rs7664664 GG GG AG rs7302091 - TT CT
rs9373570 AG AG GG rs955077 TT CT TT
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