Process of Forensic Medicine in DNA Identification of Aged Human Remains

doi:10.12116/j.issn.1004-5619.2021.511209

Abstract

Abstract:

Skeleton and teeth are important biological samples. Due to their special structure and strong ability to resist degradation, they are ideal biological materials to retain DNA under natural condition. In many cases, such as historical figure identification, aged skeleton and teeth are usually the only biological samples. However, their DNA is in a state of trace, damage and degradation to different degrees, which requires special experimental treatment to achieve identification. This paper reviews the sample selection, DNA extraction, DNA enrichment and analysis approaches based on relevant research reports in recent years, aiming to promote the further development and improvement of the aged skeleton and teeth identification system.

Key words: forensic genetics, individual identification, aged skeleton, tooth, degraded, high throughput sequencing, review

CLC Number:

Lu CHEN, Zhe ZHOU, Sheng-qi WANG. Process of Forensic Medicine in DNA Identification of Aged Human Remains[J]. Journal of Forensic Medicine, 2023, 39(5): 478-486.

References 66

1	ZIĘTKIEWICZ E， WITT M， DACA P， et al. Current genetic methodologies in the identification of disaster victims and in forensic analysis[J]. J Appl Genet，2012，53（1）：41-60. doi：10.1007/s13353-011-0068-7 .
2	ZUPANIČ PAJNIČ I， INKRET J， ZUPANC T， et al. Comparison of nuclear DNA yield and STR typing success in Second World War petrous bones and metacarpals Ⅲ[J]. Forensic Sci Int Genet，2021，55：102578. doi：10.1016/j.fsigen.2021.102578 .
3	GILL P， IVANOV P L， KIMPTON C， et al. Identification of the remains of the Romanov family by DNA analysis[J]. Nat Genet，1994，6（2）：130-135. doi：10.1038/ng0294-130 .
4	PRINZ M， CARRACEDO A， MAYR W R， et al. DNA Commission of the International Society for Forensic Genetics （ISFG）： Recommendations regarding the role of forensic genetics for disaster victim identification （DVI）[J]. Forensic Sci Int Genet，2007，1（1）：3-12. doi：10.1016/j.fsigen.2006. 10.003 .
5	EDSON S M. Getting ahead： Extraction of DNA from skeletonized cranial material and teeth[J]. J Forensic Sci，2019，64（6）：1646-1657. doi：10.1111/1556-4029.14123 .
6	HIGGINS D， AUSTIN J J. Teeth as a source of DNA for forensic identification of human remains： A review[J]. Sci Justice，2013，53（4）：433-441. doi：10.1016/j.scijus.2013.06.001 .
7	EMMONS A L， DAVOREN J， DEBRUYN J M， et al. Inter and intra-individual variation in skeletal DNA preservation in buried remains[J]. Forensic Sci Int Genet，2020，44：102193. doi：10.1016/j.fsigen.2019.102193 .
8	EDSON S M， ROSS J P， COBLE M D， et al. Naming the dead - confronting the realities of rapid identification of degraded skeletal remains[J]. Forensic Sci Rev，2004，16（1）：63-90.
9	KLAVENS A， KOLLMANN D D， ELKINS K M， et al. Comparison of DNA yield and STR profiles from the diaphysis， mid-diaphysis， and metaphysis regions of femur and tibia long bones[J]. J Forensic Sci，2021，66（3）：1104-1113. doi：10.1111/1556-4029.14657 .
10	MUNDORFF A， DAVOREN J M. Examination of DNA yield rates for different skeletal elements at increasing post mortem intervals[J]. Forensic Sci Int Genet，2014，8（1）：55-63. doi：10.1016/j.fsigen.2013.08.001 .
11	GONZALEZ A， CANNET C， ZVÉNIGOROSKY V， et al. The petrous bone： Ideal substrate in legal medicine? [J]. Forensic Sci Int Genet，2020，47：102305. doi：10.1016/j.fsigen.2020.102305 .
12	KULSTEIN G， HADRYS T， WIEGAND P. As solid as a rock-comparison of CE- and MPS-based analyses of the petrosal bone as a source of DNA for forensic identification of challenging cranial bones[J]. Int J Legal Med，2018，132（1）：13-24. doi：10.1007/s00414-017-1653-z .
13	ZUPANC T， PODOVŠOVNIK E， OBAL M， et al. High DNA yield from metatarsal and metacarpal bones from Slovenian Second World War skeletal remains[J]. Forensic Sci Int Genet，2021，51：102426. doi：10.1016/j.fsigen.2020.102426 .
14	ZUPANIČ PAJNIČ I， PETAROS A， BALAŽIC J， et al. Searching for the mother missed since the Second World War[J]. J Forensic Leg Med，2016，44：138-142. doi：10.1016/j.jflm.2016.10.015 .
15	FRISCH T， SØRENSEN M S， OVERGAARD S， et al. Volume-referent bone turnover estimated from the interlabel area fraction after sequential labeling[J]. Bone，1998，22（6）：677-682. doi：10.1016/S8756-3282（98）00050-7 .
16	GAMBA C， JONES E R， TEASDALE M D， et al. Genome flux and stasis in a five millennium transect of European prehistory[J]. Nat Commun，2014，5：5257. doi：10.1038/ncomms6257 .
17	PILLI E， VAI S， CARUSO M G， et al. Neither femur nor tooth： Petrous bone for identifying archaeological bone samples via forensic approach[J]. Forensic Sci Int，2018，283：144-149. doi：10.1016/j.forsciint.2017.12.023 .
18	PINHASI R， FERNANDES D， SIRAK K， et al. Optimal ancient DNA yields from the inner ear part of the human petrous bone[J]. PLoS One，2015，10（6）：e0129102. doi：10.1371/journal.pone.01 29102 .
19	BOŽIČ L， BENEDIK BEVC T， PODOVŠOVNIK E， et al. Intra-bone nuclear DNA variability and STR typing success in Second World War first ribs[J]. Int J Legal Med，2021，135（6）：2199-2208. doi：10.1007/s00414-021-02681-1 .
20	BENEDIK BEVC T， BOŽIČ L， PODOVŠOVNIK E， et al. Intra-bone nuclear DNA variability and STR typing success in Second World War 12th thoracic vertebrae[J]. Forensic Sci Int Genet，2021，55：102587. doi：10.1016/j.fsigen.2021.102587 .
21	OBAL M， ZUPANIČ PAJNIČ I， GORNJAK POGORELC B， et al. Different skeletal elements as a source of DNA for genetic identification of Second World War victims[J]. Forensic Sci Int Genet Suppl Ser，2019，7（1）：27-29. doi：10.1016/j.fsigss.2019.09.013 .
22	侯一平. 法医物证学[M].3版. 北京：人民卫生出版社，2009：246.
	HOU Y P. Forensic genetics[M]. 3rd ed. Beijing：People’s Medical Publishing House，2009：246.
23	HUEL R， AMORY S， BILIĆ A， et al. DNA extraction from aged skeletal samples for STR typing by capillary electrophoresis[J]. Methods Mol Biol，2012，830：185-198. doi：10.1007/978-1-61779-461-2_13 .
24	SEO S B， ZHANG A， KIM H Y， et al. Technical note： Efficiency of total demineralization and ion-exchange column for DNA extraction from bone[J]. Am J Phys Anthropol，2010，141（1）：158-162. doi：10.1002/ajpa.21193 .
25	李永久，郭磊，乔婷，等. 陈旧碎骨组织DNA检验[J].刑事技术，2017，42（3）：257-258. doi：10.16467/j.1008-3650.2017.03.021 .
	LI Y J， GUO L， QIAO T， et al. DNA test from small pieces of aged broken bones[J]. Xingshi Jishu，2017，42（3）：257-258.
26	赵斌，侯光伟，王有凤. 应用磁珠法提取陈旧骨骼DNA[J].中国法医学杂志，2014，29（3）：253-254. doi：10.13618/j.issn.1001-5728.2014.03.016 .
	ZHAO B， HOU G W， WANG Y F. DNA extraction from old bones by magnetic bead methods[J]. Zhongguo Fayixue Zazhi，2014，29（3）：253-254.
27	LOREILLE O M， DIEGOLI T M， IRWIN J A， et al. High efficiency DNA extraction from bone by total demineralization[J]. Forensic Sci Int Genet，2007，1（2）：191-195. doi：10.1016/j.fsigen.2007.02.006 .
28	WANG C C， POSTH C， FURTWÄNGLER A， et al. Genome-wide autosomal， mtDNA， and Y chromosome analysis of King Bela Ⅲ of the Hungarian Arpad dynasty[J]. Sci Rep，2021，11：19210. doi：10.1038/s41598-021-98796-x .
29	董慧婷，路志勇，焦章平，等. 不同浓度EDTA脱钙液对骨骼DNA提取效率的影响[J].中国法医学杂志，2015，30（4）：393-395. doi：10.13618/j.issn.1001-5728.2015.04.013 .
	DONG H T， LU Z Y， JIAO Z P， et al. The effects to the bone DNA extraction efficiency by different concentrations of EDTA[J]. Zhongguo Fayixue Zazhi，2015，30（4）：393-395.
30	KEMP B M， WINTERS M， MONROE C， et al. How much DNA is lost? Measuring DNA loss of short-tandem-repeat length fragments targeted by the PowerPlex 16^® system using the Qiagen MinElute Purification kit[J]. Hum Biol，2014，86（4）：313-329. doi：10.13110/humanbiology.86.4.0313 .
31	LIU Q， LIU L， ZHANG M， et al. A simple and efficient method of extracting DNA from aged bones and teeth[J]. J Forensic Sci，2018，63（3）：824-828. doi：10.1111/1556-4029.13603 .
32	CHIERTO E， CENA G， MANN R W， et al. Sweet tooth： DNA profiling of a cranium from an isolated retained root fragment[J]. J Forensic Sci，2021，66（5）：1973-1979. doi：10.1111/1556-4029. 14748 .
33	TIKALOVA E， VOTRUBOVA J， KUFNEROVA J， et al. Busting the myths： DNA typeability after 48 hours of boil[J]. Forensic Sci Int Genet Suppl Ser，2019，7（1）：79-82. doi：10.1016/j.fsigss.2019.0 9.031 .
34	PILLI E， BOCCONE S， AGOSTINO A， et al. From unknown to known： Identification of the remains at the mausoleum of fosse Ardeatine[J]. Sci Justice，2018，58（6）：469-478. doi：10.1016/j.scijus. 2018.05.007 .
35	高林林，徐念来，谢炜，等. 利用AutoMate Express^TM自动化法医DNA提取系统提取骨骼及牙齿DNA[J].法医学杂志，2013，29（2）：127-129. doi：10.3969/j.issn.1004-5619.2013.02.013 .
	GAO L L， XU N L， XIE W， et al. DNA extraction from bones and teeth using AutoMate Express^TM forensic DNA extraction system[J]. Fayixue Zazhi，2013，29（2）：127-129.
36	李斌，吕政. 利用AutoMate Express^TM系统提取陈旧性骨骼DNA[J].法医学杂志，2017，33（4）：380-382. doi：10.3969/j.issn.1004-5619.2017.04.010 .
	LI B， LÜ Z. DNA extraction from old bones by AutoMate Express^TM system[J]. Fayixue Zazhi，2017，33（4）：380-382.
37	GORDEN E M， STURK-ANDREAGGI K， MARSHALL C. Repair of DNA damage caused by cytosine deamination in mitochondrial DNA of forensic case samples[J]. Forensic Sci Int Genet，2018，34：257-264. doi：10.1016/j.fsigen.2018.02.015 .
38	RATHBUN M M， MCELHOE J A， PARSON W， et al. Considering DNA damage when interpreting mtDNA heteroplasmy in deep sequencing data[J]. Forensic Sci Int Genet，2017，26：1-11. doi：10.1016/j.fsigen.2016.09.008 .
39	HOFREITER M， JAENICKE V， SERRE D， et al. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA[J]. Nucleic Acids Res，2001，29（23）：4793-4799. doi：10.1093/nar/29.23.4793 .
40	AMBERS A， TURNBOUGH M， BENJAMIN R， et al. Assessment of the role of DNA repair in damaged forensic samples[J]. Int J Legal Med，2014，128（6）：913-921. doi：10.1007/s00414-014-1003-3 .
41	DIEGOLI T M， FARR M， CROMARTIE C， et al. An optimized protocol for forensic application of the PreC^TM Repair Mix to multiplex STR amplification of UV-damaged DNA[J]. Forensic Sci Int Genet，2012，6（4）：498-503. doi：10.1016/j.fsigen.2011.09.003 .
42	MARJANOVIĆ D， HADŽIĆ METJAHIĆ N， ČAKAR J， et al. Identification of human remains from the Second World War mass Graves uncovered in Bosnia and Herzegovina[J]. Croat Med J，2015，56（3）：257-262. doi：10.3325/cmj.2015.56.257 .
43	杨暖，刘晓云，黄肖敏. 土埋40余年股骨用于亲权鉴定的分析2例[J].广东公安科技，2021，29（2）：64-67.
	YANG N， LIU X Y， HUANG X M. Analysis of femurs buried in the ground for more than 40 years in 2 paternity testing cases[J]. Guangdong Gongan Keji，2021，29（2）：64-67.
44	ZUPANIČ PAJNIČ I， FATTORINI P. Strategy for STR typing of bones from the Second World War combining CE and NGS technology： A pilot study[J]. Forensic Sci Int Genet，2021，50：102401. doi：10.1016/j.fsigen.2020.102401 .
45	GlobalFiler^TM and GlobalFiler^TM IQC PCR Amplification Kits-PCR Amplification and CE[EB/OL]. [2021-12-20]. .
46	SMAJLOVIĆ-SKENDERAGIĆ L， IDRIZBEGOVIĆ S， BRKANIĆ L， et al. Challenges with co-amplification of microbial DNA in interpretation of STR profiles obtained from human skeletal remains[J]. Forensic Sci Int Genet，2021，51：102452. doi：10.1016/j.fsigen. 2020.102452 .
47	ZUPANIČ PAJNIČ I， GORNJAK POGORELC B， BALAŽIC J. Molecular genetic identification of skeletal remains from the Second World War Konfin I mass grave in Slovenia[J]. Int J Leg Med，2010，124（4）：307-317. doi：10.1007/s00414-010-0431-y .
48	IVANOV P L， WADHAMS M J， ROBY R K， et al. Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas Ⅱ[J]. Nat Genet，1996，12（4）：417-420. doi：10.1038/ng0496-417 .
49	ForenSeq DNA Signature Prep Reference Guide[EB/OL]. （2014-08-01）[2021-12-20]. .
50	ZHANG Q， ZHOU Z， LIU Q， et al. Evaluation of the performance of Illumina’s ForenSeq^TM system on serially degraded samples[J]. Electrophoresis，2018，39（21）：2674-2684. doi：10.1002/elps.2018 00101 .
51	SHARMA V， VAN DER PLAAT D A， LIU Y X， et al. Analyzing degraded DNA and challenging samples using the ForenSeq^TM DNA Signature Prep kit[J]. Sci Justice，2020，60（3）：243-252. doi：10.10 16/j.scijus.2019.11.004 .
52	FINAUGHTY C， REID K M， ALLI I H， et al. A first for forensic genetics in Africa： Successful identification of skeletal remains from the marine environment using massively parallel sequencing[J]. Forensic Sci Int Genet，2020，49：102370. doi：10.1016/j.fsigen.2020.102370 .
53	Web site of precision ID mtDNA whole genome Panel[EB/OL]. （2016-05-13）[2021-12-01]. .
54	WOERNER A E， AMBERS A， WENDT F R， et al. Evaluation of the precision ID mtDNA whole genome panel on two massively parallel sequencing systems[J]. Forensic Sci Int Genet，2018，36：213-224. doi：10.1016/j.fsigen.2018.07.015 .
55	PEREIRA V， LONGOBARDI A， BØRSTING C. Sequencing of mitochondrial genomes using the precision ID mtDNA whole genome panel[J]. Electrophoresis，2018，39（21）：2766-2775. doi：10.1002/elps.201800088 .
56	GORDEN E M， STURK-ANDREAGGI K， MARSHALL C. Capture enrichment and massively parallel sequencing for human identification[J]. Forensic Sci Int Genet，2021，53：102496. doi：10.1016/j.fsigen.2021.102496 .
57	CARPENTER M L， BUENROSTRO J D， VALDIOSERA C， et al. Pulling out the 1%： Whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries[J]. Am J Hum Genet，2013，93（5）：852-864. doi：10.1016/j.ajhg. 2013.10.002 .
58	YOUNG J M， HIGGINS D， AUSTIN J. Hybridization enrichment to improve forensic mitochondrial DNA analysis of highly degraded human remains[J]. Front Ecol Evol，2019，7：450. doi：10.3389/fevo.2019.00450 .
59	EDUARDOFF M， XAVIER C， STROBL C， et al. Optimized mtDNA control region primer extension capture analysis for forensically relevant samples and highly compromised mtDNA of different age and origin[J]. Genes （Basel），2017，8（10）：E237. doi：10.3390/genes8100237 .
60	TEMPLETON J E， BROTHERTON P M， LLAMAS B， et al. DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification[J]. Investig Genet，2013，4（1）：26. doi：10.1186/2041-2223-4-26 .
61	BOSE N， CARLBERG K， SENSABAUGH G， et al. Target capture enrichment of nuclear SNP markers for massively parallel sequencing of degraded and mixed samples[J]. Forensic Sci Int Genet，2018，34：186-196. doi：10.1016/j.fsigen.2018.01.010 .
62	GORDEN E M， GREYTAK E M， STURK-ANDREAGGI K， et al. Extended kinship analysis of historical remains using SNP capture[J]. Forensic Sci Int Genet，2022，57：102636. doi：10.1016/j.fsigen.2021.102636 .
63	WENDT F R， ZENG X， CHURCHILL J D， et al. Analysis of short tandem repeat and single nucleotide polymorphism loci from single-source samples using a custom HaloPlex target enrichment system panel[J]. Am J Forensic Med Pathol，2016，37（2）：99-107. doi：10.1097/paf.0000000000000228 .
64	CHO S， YU H J， HAN J， et al. Forensic application of SNP-based resequencing array for individual identification[J]. Forensic Sci Int Genet，2014，13：45-52. doi：10.1016/j.fsigen.2014.07.005 .
65	CHO S， KIM M Y， LEE J H， et al. Large-scale identification of human bone remains via SNP microarray analysis with reference SNP database[J]. Forensic Sci Int Genet，2020，47：102293. doi：10.1016/j.fsigen.2020.102293 .
66	苗春雨，徐磊，王宁，等. CT测量骨骼在法医人类学研究中的应用进展[J].法医学杂志，2017，33（1）：58-61，67. doi：10.3969/j.issn.1004-5619.2017.01.014 .
	MIAO C Y， XU L， WANG N， et al. Progress in application of measuring skeleton by CT in forensic anthropology research[J]. Fayixue Zazhi，2017，33（1）：58-61，67.

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