DNA identification of compromised samples with massive parallel sequencing

Figures & data

Table 1. Summary and comments of the result from the analysis of remains from 10 missing persons.

Case No.	Sample type (PM)	DNA concentration (ng/µL)	Reference (AM)	Result from STR analysis with CE*	LR based on the STR data	Comments on STR profile quality	Result from SNP analysis with MPS*	LR based on the SNP data	Comments on SNP profile quality
1	Femur	–	Full sibling	10/15 STRs	1.2 × 10^4	Partial DNA profile, 5 genotypes excluded due to peak height imbalance or low peak heights	122/131 SNPs	2.5 × 10^7	Partial DNA profile, 8 genotypes excluded due to low coverage and/or imbalanced allele calls
2	Tumor tissue	41	Same individual	0/15 STRs	–	No DNA profile. Low peak heights and/or >2 peaks (drop-in) per marker	96/131 SNPs	3.1 × 10^40	Partial DNA profile, 35 genotypes excluded due to low coverage and/or imbalanced allele calls
3	Fat tissue	22	Same individual	0/15 STRs	–	No DNA profile. Low peak heights and/or >2 peaks (drop-in) per marker	73/131 SNPs	3.8 × 10^30	Partial DNA profile, 58 genotypes excluded due to low coverage and/or imbalanced allele calls
4	Femur	12	Monozygotic twin	15/15 STRs	1.4 × 10^26	Full DNA profile	126/131 SNPs	1.7 × 10^54	Partial DNA profile, 5 genotypes excluded due to low coverage and/or imbalanced allele calls
5	Femur	–	Full sibling	0/15 STRs	–	Sporadic peaks, not reproducable	0/131 SNPs	–	All genotypes excluded due to low coverage and/or imbalanced allele calls
6	Femur	–	Same individual	0/15 STRs	–	Sporadic peaks, not reproducible	0/131 SNPs	–	All genotypes excluded due to low coverage and/or imbalanced allele calls
7	Femur	6	No reference material	0/15 STRs	–	Sporadic peaks, not reproducible	67/131 SNPs	–	Partial DNA profile, 8 genotypes excluded due to low coverage and/or imbalanced allele calls
8	Femur	100	Parent/child	15/15 STRs	7.0 × 10^5	Full DNA profile	130/131 SNPs	4.3 × 10^10	Partial DNA profile, 1 genotype excluded due to low coverage and/or imbalanced allele calls
9	Femur	20	Parent/child	15/15 STRs	2.3 × 10^5	Full DNA profile	131/131 SNPs	1.5 × 10^12	Full DNA profile
10	Femur	3	Half-uncle	15/15 STRs	12	Full DNA profile	131/131 SNPs	40	Full DNA profile

PM: postmortem; AM: antemortem; STR: short tandem repeat; CE: capillary electrophoresis; LR: likelihood ratio; MPS: massive parallel sequencing; SNP: single nucleotide polymorphism; –: not detectable; *Number of markers that met the quality criteria/Number of markers included in the analysis.

Figure 1. Mean and standard deviation of the coverage for each of the single nucleotide polymorphism (SNP) marker included in the analysis using massive parallel sequencing (MPS). The chart is based on the eight postmortem (PM) samples that resulted in full or partial SNP profiles.

Figure 2. Sample and marker specific coverage for the eight postmortem (PM) samples that resulted in full or partial single nucleotide polymorphism (SNP) profiles for the massive parallel sequencing (MPS) analysis. A coverage of 200× was used as a minimum threshold for genotype calling.

Figure 3. Sample and marker specific allele read frequency (ARF) for the eight postmortem (PM) samples that resulted in full or partial single nucleotide polymorphism (SNP) profiles for the massive parallel sequencing (MPS) analysis. An ARF values between 0.4 and 0.6 resulted in a heterozygous genotype and an ARF value between 0 and 0.1 or between 0.9 and 1 resulted in a homozygous genotype.