Genetic Analysis using the Applied Biosystems™ Precision ID Ancestry Panel markers of seven ...

30 Pages·2017·5.58 MB·English

Genetic analysis of Applied Biosystems™ Prec
ision ID Ancestry Panel for Seven Asian Popula
tions
1
Index
1.  Introduction
2.  Workflow
3.  Results
4.  Discussion
2
Asian Ancestry
Royal CD et al. Inferring Genetic Ancestry: Opportunities, Challenges,
and Implications. Am J Hum Genet. 2010;86(5):661-73.
3
O b j e c t s
Objects
Evaluating the performance of the Applied Biosystems™ Precision ID
Ancestry Panel for seven population in Asia
Assessing the accuracy and reliability of the HID SNP Genotyper plugin of
the Torrent Server.
Providing the SNP data of 750 people in Asia
4
W o r k f l o w
•  Applied Biosystems™ Precision ID Ancestry Panel
Specifications
Targets 165 single-nucleotide polymorphisms (SNPs)
Average 130 bp for the 55 SNPs from
Dr. Kenneth Kidd
Amplicon length
Average 120 bp for the 123 SNPs from
Dr. Michael Seldin
Primer pool size 165 primer pairs in 1 tube
Input DNA 1 ng
5
W o r k f l o w
•  Solutions for forensic DNA analysis
•  Simplest targeted NGS workflow
6
W o r k f l o w
•  Asian Subgrouping
Geographical region Population sample description N
Northeast Asia Han Chinese South [CHS] 99
Han Chinese in Beijing, China [CHB] 100
Japanese in Tokyo, Japan [JPT] 101
Korean from Seoul, Korea 100
Southeast Asia Kinh in Ho Chi Minh City, Vietnam [KHV] 100
Southwest Asia Nepalese 100
Indian 51
Pakistani in Pathan, Pakistan 49
Punjabi in Lahore, Pakistan 50
7
750
R e s u l t s
•  SNP coverage
-  Coverage varied from 193× (rs1407434) to 5369× (rs2073821)
-  With an average of 1918×
8
R e s u l t s
•  NOC - the coverage for the locus is less than twice the standard deviation of th
e mean coverage for the sample
Chrom Position Target ID Genotype Coverage A Reads C Reads G Reads T Reads
chr3 1.21E+08 rs12498138 - 0 0 0 0 0
chr12 1.09E+08 rs2070586 - 0 0 0 0 0
chr8 1.22E+08 rs2196051 - 0 0 0 0 0
chr12 17407792 rs1513056 NN 920 97 0 823 0
chr13 34847737 rs7997709 NN 1487 0 1342 0 145
chr14 20818131 rs1760921 NN 1509 2 155 1 1351
-  Of the 123,750 genotypes (750people x 165 SNP markers)
-  123,431 (99.7%) were called, 6 (0.005%) with no coverage
-  318 (0.26%) called as ‘NOC’
-  Average depth of 318 SNPs; 94.4x
9
R e s u l t s
•  NOC
•  rs12498138 failed to type 58 of 750 with an average of 9.6×
Pop Chrom Position Target ID Genotype Coverage A Reads C Reads G Reads T Reads
Korean chr3 1.21E+08 rs12498138 - 0 0 0 0 0
Han chr3 1.21E+08 rs12498138 NN 1 0 0 1 0
India chr3 1.21E+08 rs12498138 NN 1 0 0 1 0
Pathan chr3 121459589 rs12498138 NN 21 0 0 21 0
Vietnam chr3 121459589 rs12498138 NN 22 0 0 22 0
Punjab chr3 121459589 rs12498138 NN 28 1 0 27 0
•  rs2196051 failed to type 42 of 750 with an average of 7.1×
Pop Chrom Position Target ID Genotype Coverage A Reads C Reads G Reads T Reads
Korean chr8 122124302 rs2196051 - 0 0 0 0 0
India chr8 122124302 rs2196051 - 0 0 0 0 0
Vietnam chr8 122124302 rs2196051 NN 1 0 0 1 0
Pathan chr8 122124302 rs2196051 NN 4 1 0 3 0
India chr8 122124302 rs2196051 NN 5 0 0 5 0
Punjab chr8 122124302 rs2196051 NN 193 9 0 184 0
10