Comparison of target enrichment strategies for ancient pathogen DNA

Furtwängler A; Neukamm J; Böhme L; Reiter E; Vollstedt M; Arora N; Singh P; Cole ST; Knauf S; Calvignac-Spencer S; Krause-Kyora B; Krause J; Schuenemann VJ; Herbig A

doi:10.2144/btn-2020-0100

Research Publication

Comparison of target enrichment strategies for ancient pathogen DNA

Furtwängler A, Neukamm J, Böhme L et al.

33135465 PubMed ID

14 Authors

2020 Dec Published

98 Samples

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Chapter I

Publication Details

Comprehensive information about this research publication

Authors 14 researchers

Publication Date 2020 Dec

URL https://pubmed.ncbi.nlm.nih.gov/33135465/

Authors

FA

Furtwängler A

NJ

Neukamm J

BL

Böhme L

RE

Reiter E

VM

Vollstedt M

AN

Arora N

SP

Singh P

CS

Cole ST

KS

Knauf S

CS

Calvignac-Spencer S

KB

Krause-Kyora B

KJ

Krause J

SV

Schuenemann VJ

HA

Herbig A

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Chapter II

Abstract

Summary of the research findings

In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods - array-based hybridization capture and in-solution capture using either RNA or DNA baits - have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits.

Chapter III

Ancient DNA Samples

98 ancient DNA samples referenced in this publication

98 Samples

Sample ID	Date/Era	Country	Locality	Sex	mtDNA	Y-DNA
TU918(SX32)	2461 BCE	France	Alsace. Lingolsheim	M	`N1`	`R-P310`
TU919(SX33)	4780 BCE	France	Alsace. Lingolsheim	M	`H1`	`I-L161`
TU915(SX29)	4800 BCE	France	Alsace. Lingolsheim	M	`T2b`	`I-M423`
TU916(SX30)	4789 BCE	France	Alsace. Lingolsheim	F	`U8b1b1`
MX259	2453 BCE	Germany	Southern Germany. Anselfingen	M	`K1a3a`	`R-BY61838`
MX270	2250 BCE	Germany	Southern Germany. Singen	M	`W3a1`	`R-L20`
MX275	2136 BCE	Germany	Southern Germany. Singen	M	`W3a1`	`R-L2`
MX277	1936 BCE	Germany	Southern Germany. Singen	F	`H5a1`
MX279	1882 BCE	Germany	Southern Germany. Singen	M	`H76a`	`R-L2`
MX280	2111 BCE	Germany	Southern Germany. Singen	F	`U5a1`
MX283	2127 BCE	Germany	Southern Germany. Singen	M	`H-c`	`R-L2`
MX288	2201 BCE	Germany	Southern Germany. Singen	M	`K1a1a`	`R-L2`
MX251	2199 BCE	Germany	Southern Germany. Singen	F	`K1a1a`
MX252	1945 BCE	Germany	Southern Germany. Singen	M	`H83`	`R-L2`
MX254	2250 BCE	Germany	Southern Germany. Singen	M	`H-c`	`R-L2`
MX256	2135 BCE	Germany	Southern Germany. Singen	F	`H-c`
MX257	1880 BCE	Germany	Southern Germany. Singen	M	`U4a1a`	`R-L2`
MX258	2029 BCE	Germany	Southern Germany. Singen	M	`U5b1-a`	`R-P312`
MX286	2035 BCE	Germany	Southern Germany. Singen	M	`K1a1a`	`R-L2`
MX283	2127 BCE	Germany	Southern Germany. Singen	M	`H-c`	`R-L2`
MX286	2035 BCE	Germany	Southern Germany. Singen	M	`K1a1a`	`R-L2`
MX265	757 BCE	Germany	Southern Germany. Singen	M	`H1c`	`R-M458`
TU876(SX10)	2750 BCE	Switzerland	Rapperswil Zürichstrasse	F	`U3a1`
TU874(SX8)	2695 BCE	Switzerland	Rapperswil Zürichstrasse	F	`U3a1`
RA54	2660 BCE	Switzerland	Seengen	F	`J2b1a2`
MX193	2283 BCE	Switzerland	Spreitenbach CWC	F	`K1a-a4`
TU908(SX21)	2461 BCE	Switzerland	Wartau	F	`H3`
TU910(SX22)	3092 BCE	Switzerland	Wartau	F	`K1a4a1`
TU904(SX17)	2467 BCE	Switzerland	Wartau	F	`U4a2f`
TU914(SX26)	2461 BCE	Switzerland	Wartau	F	`K2b1`
MX304	2900 BCE	Switzerland	Auvernier	M		`R-P310`
MX310	2862 BCE	Switzerland	Burgäschisee	M		`R-M269`
MX195	2464 BCE	Switzerland	Spreitenbach CWC	M	`H11a-a`	`I-L161`
MX196	2627 BCE	Switzerland	Spreitenbach CWC	F	`J1c3`
MX197	2557 BCE	Switzerland	Spreitenbach CWC	F	`H11a-a`
MX198	2861 BCE	Switzerland	Spreitenbach CWC	F	`J1c4`
MX199	2454 BCE	Switzerland	Spreitenbach CWC	F	`J2b1a`
MX188	2566 BCE	Switzerland	Spreitenbach CWC	M	`U2e2a1d`	`I-L161`
MX189	2199 BCE	Switzerland	Spreitenbach CWC	F	`T2b`
MX190	2855 BCE	Switzerland	Spreitenbach CWC	M	`U2e2a1d`	`I-CTS5375`
MX191	2837 BCE	Switzerland	Spreitenbach CWC	M	`H3-c`	`I-CTS5375`
MX192	2571 BCE	Switzerland	Spreitenbach CWC	M	`H11a-a`	`I-CTS5375`
MX298	2622 BCE	Switzerland	Wartau	M	`X2b4`	`G-PF3146`
TU905(SX18)	172 BCE	Switzerland	Wartau	F	`B4c1b2c2`
TU907(SX20)	1733 BCE	Switzerland	Wartau	M	`K1a4a1`	`R-P312`
TU911(SX23)	1882 BCE	Switzerland	Wartau	F	`X2b4`
RA63	2131 BCE	Switzerland	Zuzach	M	`H5a`	`R-L2`
RA64	2274 BCE	Switzerland	Zuzach	M	`K1a1`	`R-L2`
Aes1	3090 BCE	Switzerland	Aesch	M	`H1-d`	`G-L166`
Aes10	2912 BCE	Switzerland	Aesch	F	`K1a-a4`
Aes11	3011 BCE	Switzerland	Aesch	F	`K1a3a`
Aes12	3010 BCE	Switzerland	Aesch	M	`H1`	`G-L166`
Aes13	3013 BCE	Switzerland	Aesch	M	`X2b-a`	`G-L166`
Aes14	3012 BCE	Switzerland	Aesch	M	`U5a1c1`	`G-L166`
Aes15	3012 BCE	Switzerland	Aesch	F	`U5a1c1`
Aes16	3091 BCE	Switzerland	Aesch	F	`K1a2`
Aes17	3011 BCE	Switzerland	Aesch	M	`H10-a`	`G-L166`
Aes18	2916 BCE	Switzerland	Aesch	F	`H3`
Aes19	3100 BCE	Switzerland	Aesch	M	`H1`	`G-L166`
Aes2	3011 BCE	Switzerland	Aesch	F	`H1`
Aes20	2917 BCE	Switzerland	Aesch	M	`K2b1a`	`G-L166`
Aes21	3100 BCE	Switzerland	Aesch	M	`U8b1b`	`G-L166`
Aes22	2892 BCE	Switzerland	Aesch	M	`J2b1a2`	`G-L166`
Aes23	2885 BCE	Switzerland	Aesch	M	`J2b1a`	`G-L166`
Aes24	2915 BCE	Switzerland	Aesch	M	`K2b1a`	`G-Z6488`
Aes25	2865 BCE	Switzerland	Aesch	M	`X2b-a`	`R-L151`
Aes3	3075 BCE	Switzerland	Aesch	F	`H1`
Aes4	3098 BCE	Switzerland	Aesch	M	`H3`	`G-L166`
Aes5	3016 BCE	Switzerland	Aesch	F	`J1c3`
Aes8	2921 BCE	Switzerland	Aesch	F	`J1c3`
Aes9	2917 BCE	Switzerland	Aesch	F	`U5b2b5`
Aes6	2905 BCE	Switzerland	Aesch	M	`H5`	`G-L166`
Aes7	3100 BCE	Switzerland	Aesch	M	`U5b2b2`	`G-L166`
RA57	2906 BCE	Switzerland	Muttenz	F	`J2b1a2`
RA58	3010 BCE	Switzerland	Muttenz	M	`H7d`	`G-Z6488`
RA59.Furtwangler	2898 BCE	Switzerland	Muttenz	F	`H1-f`
RA61	2906 BCE	Switzerland	Muttenz	M	`K1a4a1`	`G-L166`
RA62	2923 BCE	Switzerland	Muttenz	M	`H1-f`	`G-L166`
TU877(SX11)	4455 BCE	Switzerland	Niederried Ursisbalm	F	`J1c1b`
TU875(SX9)	4445 BCE	Switzerland	Niederried Ursisbalm	F	`H5`
RA42	3341 BCE	Switzerland	Oberbipp Horgen	F	`H3ap`
RA43	3331 BCE	Switzerland	Oberbipp Horgen	F	`K1a4a1a`
RA44	2913 BCE	Switzerland	Oberbipp Horgen	F	`K1a-a4`
RA45	3098 BCE	Switzerland	Oberbipp Horgen	F	`H1`
MX299	2910 BCE	Switzerland	Oberbipp Horgen	M
MX150	3350 BCE	Switzerland	Oberbipp Horgen	M	`H4a1a`	`G-L91`
MX182	3341 BCE	Switzerland	Oberbipp Horgen	M	`K1-a`	`G-PF3239`
MX183	3344 BCE	Switzerland	Oberbipp Horgen	M	`K1a-a4`	`G-PF3239`
MX184	3400 BCE	Switzerland	Oberbipp Horgen	F	`J1c3`
MX187	3337 BCE	Switzerland	Oberbipp Horgen	M	`K1a-a4`	`G-L166`
MX203	3400 BCE	Switzerland	Oberbipp Horgen	F	`H4a1`
MX204	3400 BCE	Switzerland	Oberbipp Horgen	M	`K1a2b`	`G-Z6488`
MX209	3400 BCE	Switzerland	Oberbipp Horgen	M	`K1a-a4`	`G-L166`
MX210	3400 BCE	Switzerland	Oberbipp Horgen	M	`K1a2b`	`G-L166`
MX211	3264 BCE	Switzerland	Oberbipp Horgen	M	`K1a-a4`	`G-L166`
MX212	3341 BCE	Switzerland	Oberbipp Horgen	M	`H1`	`G-L166`
MX213	3365 BCE	Switzerland	Oberbipp Horgen	M	`K1b1a`	`G-L166`
MX219	3331 BCE	Switzerland	Oberbipp Horgen	M	`K`	`G-PF3146`

Chapter IV

Analysis

Comprehensive review of ancestry and genetic findings

Important Disclaimer: This review has been performed semi-automatically and is provided for informational purposes only. While we strive for accuracy, this analysis may contain errors, omissions, or misinterpretations of the original research. DNA Genics disclaims all liability for any inaccuracies, errors, or consequences arising from the use of this information. Users should independently verify all information and consult original research publications before making any decisions based on this content. This analysis is not intended as a substitute for professional scientific review or medical advice.

Comparison of target enrichment strategies for ancient pathogen DNA

Publication Details

Authors

Abstract

Ancient DNA Samples

Analysis

Analysis In Progress

Summary

Key Findings

Ancestry Insights

Traits Analysis

Historical Context

Scientific Assessment

Explore More Research

Comparison of target enrichment strategies for ancient pathogen DNA

Publication Details

Authors

Abstract

Ancient DNA Samples

Analysis

Analysis In Progress

Summary

Key Findings

Ancestry Insights

Traits Analysis

Historical Context

Scientific Assessment

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