RCO

10-31-2017, 04:48 PM

Defining Y-SNP variation among the Flemish population (Western Europe) by full genome sequencing

Maarten H.D.Larmuseau, Gilles P.P.L.Otten, Ronny Decorte, Philip Van Damme, MatthieuMoissede

Highlights:

Population-wide data of forensic relevant Y-SNPs are lacking.

A representative sample of 270 full Y chromosomes from Flemish males is collected.

Based on the full Y chromosomes, the Y-SNP variation in Flanders is characterised.

Y-SNP variation is covered according to the latest minimal reference Y-tree.

Recommendations for future population samples for Y-SNPs are discussed.

Abstract

Y-chromosomal single nucleotide polymorphisms (Y-SNPs) represent a powerful tool in forensic research and casework, especially for inferring paternal ancestry of unknown perpetrators and unidentified bodies. However, the wealth of recently discovered Y-SNPs, the ‘jungle’ of different evolutionary lineage trees and nomenclatures, and the lack of population-wide data of many phylogenetically mapped Y-SNPs, limits the use of Y-SNPs in routine forensic approaches. Recently, a concise reference phylogeny of the human Y chromosome, the ‘Minimal Reference Y-tree’, was introduced aiming to provide a stable phylogeny with optimal global discrimination capacity by including the most resolving Y-SNPs. Here, we obtained a representative sample of 270 whole-genome sequences (WGS) to grasp the Y-SNP variation within the autochthonous Flemish population (Belgium, Western Europe) according to this reference Y-tree. The high quality of the Y-SNP calling was guaranteed for the WGS sample as well as its representativeness for the Flemish population based on the comparison of the main haplogroup frequencies with those from earlier studies on Flanders and the Netherlands. The 270 Flemish Y chromosomes were assigned to 98 different sub-haplogroups of the Minimal Reference Y-tree, showing its high potential of discrimination and confirming the spectrum of evolutionary lineages within Western Europe in general and within Flanders in particular. The full database with all Y-SNP calls of the Flemish sample is public available for future updates including forensic and population genetic studies. New initiatives to categorise Y-SNP variation in other populations according to the reference phylogeny of the Y chromosome are highly encouraged for forensic applications. Recommendations to realise such future population sample sets are discussed based on this study.

Keywords

Next-generation sequencing, Full Y chromosome, Y-SNPs, AMY-tree, Belgium

Haplogroup Sub-haplogroup Minimal Reference Y-tree N

A A1-M31 1

E1b1b E-V65 1

E1b1b E-V13 7

E1b1b E-M34*(xM84) 1

G G-Z738*(xCTS4803) 2

G G-CTS4803 4

G G-PF3359 2

I1 I-M253*(xZ131,DF29) 2

I1 I-L22*(xP109,Z74) 5

I1 I-P109 2

I1 I-Z74*(L813) 1

I1 I-Z59*(xZ60,Z2040) 5

I1 I-Z60*(xZ2539,Z140) 1

I1 I-Z2539 4

I1 I-Z140 4

I1 I-Z138 4

I1 I-Z63*(xL1237) 3

I1 I-L1237 1

I2 I-CTS595*(xM26,L1286) 1

I2 I-M26 2

I2 I-L1286 1

I2 I-L38 2

I2 I-M284 2

I2 I-L1229 4

I2 I-L701 1

I2 I-L801*(xCTS1977,CTS6433) 3

I2 I-CTS1977 4

I2 I-CTS6433*(xZ78) 2

I2 I-Z78 1

J1 J-FGC6064 1

J1 J-PF7264 1

J1 J-FGC11 1

J2a J-Z438 5

J2a J-Z6065 2

J2a J-Z500*(xM92) 1

J2a J-M92 1

J2a J-L227 1

J2a J-Z7671 1

J2b J-L283 4

Q Q-L245 1

R1a R-Z283*(xM458,Z91,Z284) 1

R1a R-Z92 1

R1a R-CTS3402*(xL365) 1

R1a R-L448 1

R1a R-Z2122*(xM582) 1

R1a R-M582 1

R1a R-Z2125 2

R1b R-L389*(xP297) 1

R1b R-M269*(xL23) 1

R1b R-Z2103 3

R1b R-M412*(xL11) 1

R1b R-L11*(xU106,P312) 6

R1b R-U106*(xZ8057,Z18,Z381,FGC396) 2

R1b R-Z18 5

R1b R-Z156 21

R1b R-Z301*(xU198,L48) 3

R1b R-U198 2

R1b R-L48*(xL47,Z9) 3

R1b R-L47 5

R1b R-Z9*(xZ30,Z331) 1

R1b R-Z30 12

R1b R-Z331 7

R1b R-FGC396 1

R1b R-P312*(xL238,DF19,DF99,DF27,U152,M529) 1

R1b R-DF19 10

R1b R-DF99 1

R1b R-DF27*(xZ225,Z2552,Z2557,Z2560,Z31644,Z34609,Z195) 6

R1b R-Z225 1

R1b R-Z2552 1

R1b R-Z2557 1

R1b R-Z34609 3

R1b R-Z209*(xZ216,CTS4065) 4

R1b R-Z216*(xZ214) 1

R1b R-CTS4065 1

R1b R-Z198*(xZ262) 1

R1b R-Z262 3

R1b R-U152*(xL2,Z36,Z56,Z192) 4

R1b R-L2*(xZ367,Z49) 7

R1b R-Z34 1

R1b R-Z49*(xZ142) 5

R1b R-Z142 3

R1b R-Z36 2

R1b R-Z56*(xS47,Z144) 1

R1b R-S47 3

R1b R-Z144 1

R1b R-Z192 3

R1b R-M529*(xDF63,DF13) 2

R1b R-DF63 1

R1b R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) 11

R1b R-DF21*(xP314,Z246,S3058) 1

R1b R-DF41 2

R1b R-DF49*(xDF23) 2

R1b R-L513 3

R1b R-Z251 3

R1b R-Z2534 3

L L-M357*(xM2398) 1

T T-Z709 1

T T-L131 2

Total 270

http://www.sciencedirect.com/science/article/pii/S187249731730220X

Maarten H.D.Larmuseau, Gilles P.P.L.Otten, Ronny Decorte, Philip Van Damme, MatthieuMoissede

Highlights:

Population-wide data of forensic relevant Y-SNPs are lacking.

A representative sample of 270 full Y chromosomes from Flemish males is collected.

Based on the full Y chromosomes, the Y-SNP variation in Flanders is characterised.

Y-SNP variation is covered according to the latest minimal reference Y-tree.

Recommendations for future population samples for Y-SNPs are discussed.

Abstract

Y-chromosomal single nucleotide polymorphisms (Y-SNPs) represent a powerful tool in forensic research and casework, especially for inferring paternal ancestry of unknown perpetrators and unidentified bodies. However, the wealth of recently discovered Y-SNPs, the ‘jungle’ of different evolutionary lineage trees and nomenclatures, and the lack of population-wide data of many phylogenetically mapped Y-SNPs, limits the use of Y-SNPs in routine forensic approaches. Recently, a concise reference phylogeny of the human Y chromosome, the ‘Minimal Reference Y-tree’, was introduced aiming to provide a stable phylogeny with optimal global discrimination capacity by including the most resolving Y-SNPs. Here, we obtained a representative sample of 270 whole-genome sequences (WGS) to grasp the Y-SNP variation within the autochthonous Flemish population (Belgium, Western Europe) according to this reference Y-tree. The high quality of the Y-SNP calling was guaranteed for the WGS sample as well as its representativeness for the Flemish population based on the comparison of the main haplogroup frequencies with those from earlier studies on Flanders and the Netherlands. The 270 Flemish Y chromosomes were assigned to 98 different sub-haplogroups of the Minimal Reference Y-tree, showing its high potential of discrimination and confirming the spectrum of evolutionary lineages within Western Europe in general and within Flanders in particular. The full database with all Y-SNP calls of the Flemish sample is public available for future updates including forensic and population genetic studies. New initiatives to categorise Y-SNP variation in other populations according to the reference phylogeny of the Y chromosome are highly encouraged for forensic applications. Recommendations to realise such future population sample sets are discussed based on this study.

Keywords

Next-generation sequencing, Full Y chromosome, Y-SNPs, AMY-tree, Belgium

Haplogroup Sub-haplogroup Minimal Reference Y-tree N

A A1-M31 1

E1b1b E-V65 1

E1b1b E-V13 7

E1b1b E-M34*(xM84) 1

G G-Z738*(xCTS4803) 2

G G-CTS4803 4

G G-PF3359 2

I1 I-M253*(xZ131,DF29) 2

I1 I-L22*(xP109,Z74) 5

I1 I-P109 2

I1 I-Z74*(L813) 1

I1 I-Z59*(xZ60,Z2040) 5

I1 I-Z60*(xZ2539,Z140) 1

I1 I-Z2539 4

I1 I-Z140 4

I1 I-Z138 4

I1 I-Z63*(xL1237) 3

I1 I-L1237 1

I2 I-CTS595*(xM26,L1286) 1

I2 I-M26 2

I2 I-L1286 1

I2 I-L38 2

I2 I-M284 2

I2 I-L1229 4

I2 I-L701 1

I2 I-L801*(xCTS1977,CTS6433) 3

I2 I-CTS1977 4

I2 I-CTS6433*(xZ78) 2

I2 I-Z78 1

J1 J-FGC6064 1

J1 J-PF7264 1

J1 J-FGC11 1

J2a J-Z438 5

J2a J-Z6065 2

J2a J-Z500*(xM92) 1

J2a J-M92 1

J2a J-L227 1

J2a J-Z7671 1

J2b J-L283 4

Q Q-L245 1

R1a R-Z283*(xM458,Z91,Z284) 1

R1a R-Z92 1

R1a R-CTS3402*(xL365) 1

R1a R-L448 1

R1a R-Z2122*(xM582) 1

R1a R-M582 1

R1a R-Z2125 2

R1b R-L389*(xP297) 1

R1b R-M269*(xL23) 1

R1b R-Z2103 3

R1b R-M412*(xL11) 1

R1b R-L11*(xU106,P312) 6

R1b R-U106*(xZ8057,Z18,Z381,FGC396) 2

R1b R-Z18 5

R1b R-Z156 21

R1b R-Z301*(xU198,L48) 3

R1b R-U198 2

R1b R-L48*(xL47,Z9) 3

R1b R-L47 5

R1b R-Z9*(xZ30,Z331) 1

R1b R-Z30 12

R1b R-Z331 7

R1b R-FGC396 1

R1b R-P312*(xL238,DF19,DF99,DF27,U152,M529) 1

R1b R-DF19 10

R1b R-DF99 1

R1b R-DF27*(xZ225,Z2552,Z2557,Z2560,Z31644,Z34609,Z195) 6

R1b R-Z225 1

R1b R-Z2552 1

R1b R-Z2557 1

R1b R-Z34609 3

R1b R-Z209*(xZ216,CTS4065) 4

R1b R-Z216*(xZ214) 1

R1b R-CTS4065 1

R1b R-Z198*(xZ262) 1

R1b R-Z262 3

R1b R-U152*(xL2,Z36,Z56,Z192) 4

R1b R-L2*(xZ367,Z49) 7

R1b R-Z34 1

R1b R-Z49*(xZ142) 5

R1b R-Z142 3

R1b R-Z36 2

R1b R-Z56*(xS47,Z144) 1

R1b R-S47 3

R1b R-Z144 1

R1b R-Z192 3

R1b R-M529*(xDF63,DF13) 2

R1b R-DF63 1

R1b R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) 11

R1b R-DF21*(xP314,Z246,S3058) 1

R1b R-DF41 2

R1b R-DF49*(xDF23) 2

R1b R-L513 3

R1b R-Z251 3

R1b R-Z2534 3

L L-M357*(xM2398) 1

T T-Z709 1

T T-L131 2

Total 270

http://www.sciencedirect.com/science/article/pii/S187249731730220X