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xGen Sample Identification (ID) Amplicon Panel

Track and manage samples, including matched pairs

The power of discrimination of this amplicon panel is over 1 in 85,000, making it suitable for longitudinal research studies and scenarios in which genetic fingerprinting is relevant to research design and analysis.

xGen NGS—made for sample identification research.

Ordering

  • Easily track samples within and between studies
  • Ideal for confirming research on tumor/normal pairs
  • Power of discrimination over 1 in 85,000 [1]
  • Reliable calling of germline variants
  • Complements both WGS and exome sequencing for sample tracking
  • On-target coverage uniformity >95%
  • Leverages the high fidelity of Illumina® platforms
  • Complete library generation in a single kit
  • Reduce sequencing cost with 1536 indexing

For customers who wish to purchase the legacy rhAmpSeq Sample ID Panel, please contact us today.

Product details

The xGenTM Sample ID Amplicon Panel is a streamlined amplicon NGS prep kit that includes 95 primer pairs targeting exonic single nucleotide polymorphisms (SNPs) with high minor allele frequency (MAF) and 9 amplicons to determine gender. This panel is compatible with circulating, cell-free DNA, as well as FFPE samples. With the advent of liquid biopsy assays of circulating nucleic acids in oncology research studies, proper tracking of samples has become increasingly critical. This panel represents a powerful and reliable method for tracking and identifying markers in a variety of sample types including liquid biopsy samples.

The power of discrimination of this panel is over 1 in 85,000 [1], making this product suitable for longitudinal studies and scenarios in which genetic fingerprinting is relevant to research design and analysis in various areas including genotyping, research on noninvasive prenatal testing (NIPT), research on transplant rejection, and others. This product is a complete kit that includes all elements necessary to generate multiplex libraries compatible with Illumina® sequencing platforms, including primer pairs and indexed sequencing adapters. 

As seen in Figure 1, xGen Custom Amplicon Panels have a single tube workflow that is done in as little as 2 hours.

Figure 1. xGen Custom Amplicon Panels have a single tube workflow that is done in as little as 2 hours. Creating an NGS library starts with a multiplex PCR reaction. Your custom panel is combined with the DNA sample to amplify the targets of interest. The samples are then amplified with indexing primers to create a functional dual indexed library. As an optional step, the xGen Normalase reagent can be used after pooling multiple libraries to ensure each is equally represented in the final sample for the flowcell.

Specifications

FeaturesxGenTM Sample ID Amplicon Panel
Input DNA required 10–25 ng
Time required 2 hours
Number of amplicons 104
Amplicon size 120–160 (Average 145 bp)
On target percentage >95%
Coverage uniformity at > 20% of mean >95%
Multiplexing on MiSeq® v2 Nano at 500X depth 38 Samples
Multiplexing on MiSeq® v2 at 750X depth 384 Samples
Sample compatibility cfDNA and FFPE

Product data

Table 1. Reliable results across variety of ethnic backgrounds and gender

DNA Gender Race/ethnicity % On target % Coverage uniformity
NA00897 M Caucasian 99.7 98.2
NA11496 F Caucasian 96.2 100
NA14624 M Caucasian 99.9 93.3
NA24143 F Caucasian (Ashkenazi) 99.8 93.4
NA14639 F Caucasian (Ashkenazi) 99.9 93.3
NA14628 F Caucasian (English/German) 99.9 93.3
NA14637 F Caucasian (French Canadian) 99.9 94.5
NA14634 M Caucasian (Norwegian) 99.9 95.6
NA12878 F Caucasian (Utah/Mormon) 99.8 99.3
NA12249 F Caucasian (Utah/Mormon) 99.9 93.3
HG02190 F Chinese (Dai) 99.9 93.3
NA24695 F Chinese (Han) 99.9 92.2
NA19240 F Yoruban 99.7 97.1

Sequencing metrics for the xGen Sample ID Amplicon Panel with an array of Coriell repository DNA samples (10 ng input each) of different ethnicities and genders. Libraries were sequenced on a MiniSeq® (Illumina) instrument. On-target and coverage uniformity were calculated as per base.

ChrPOSSNP IDREFALTCoriell NA1278Coriell NA00897Coriell NA11496
167861520rs2229546CA 100%52%
1158582646rs2251969TC  100%
1167849414rs203849AG50%100% 
1179520506rs1410592GA100%53%100%
1209811886rs2076356TG53% 52%
1209968684rs2013162CA100% 47%
1228431095rs1771455AG47%100%53%
244502788rs3738985AC100%100%100%
249381585rs1394205CT47%  
275115108rs10194657AG  50%
2169789016rs497692TC 100% 
2170092395rs2229267AG52%47%51%
2179454394rs1560221AG 47%48%
2179455207rs2163009TC 45%48%
2215820013rs10498027GA45%  
2219941063rs897477GA100%100%100%
2227896976rs10203363CT 100%46%
34403767rs2819561AG50%100%51%
34712413rs2306875GA48%52%45%
345989044rs2234358TG49%100% 
3148727133rs4938GA52%51%46%
45749904rs386594666TC 50%49%
486844835rs6824722AG47%  
486915848rs10003909TC51% 50%
488534235rs2736982AG100% 100%
513719022rs30169TG100%100%48%
513829799rs1348689GA50%50%100%
555155402rs1009639CT99%99%99%
582834630rs309557TC 53%54%
5135392426rs4669TC 48% 
5138456815rs3088052TC48%52%52%
6146755140rs2942GA46%47%49%
6152464839rs2256135AG51%52%49%
734009946rs10265207CT100% 99%
748450157rs17548783TC47%100% 
750742180rs1800504CT50%50%100%
7100804140rs1048303CT52%100% 
7127250907rs386607686TC46%100%100%
894935937rs4735258TC100% 51%
8104337096rs3808554AG48%47%45%
927202870rs386602523AG50% 46%
977415284rs7859201AC100%  
997365642rs9695GA47%51% 
9100190780rs1381532AG100% 100%
9104184022rs4577GA100%  
9136304497rs3124768AG100%47%52%
1069926097rs2673794TC47%100% 
1073856984rs3312AG 45% 
1078944590rs1131824GA47%49%100%
1085972043rs10749482AG51%47%46%
1095791763rs17109674GA  50%
10104596924rs6163CA 47% 
10104814162rs2275271TC46%  
10105819956rs805701GA100%100%100%
10113920465rs2277207GA48%47%47%
116629665rs1043388CT  47%
1116133413rs4617548AG100% 45%
1130255185rs386601843CT51%48%100%
12993930rs7300444CT   
128757481rs2028373GA 53%41%
1252200742rs60637CA50%100%100%
1450769717rs2297995GA 100%100%
1464637147rs7161192CA 47% 
1474992800rs699374AG51% 45%
1476045858rs2287016GA   
1534528948rs4577050GA100%47%46%
1589401615rs3825994TG100%48%100%
1589402596rs698621TG53%48%100%
1668713730rs2296409GA51%100%100%
1668713823rs2296408CA49%100%100%
1668729785rs17715450CA48%100%100%
1670303580rs2070203GA47%48%46%
1670546234rs3762171GA48%45%50%
177192091rs222842CT47%100%100%
1710536018rs2285479GA100% 100%
1710542471rs2285475TG100% 100%
1742449789rs5910GA100%48% 
1771192663rs1052706GA100%51%55%
1771192873rs11544800AG100%53%52%
1771197748rs1037256GA100%49%56%
1812351342rs11080572CT47%100%52%
1847455923rs2298628CT48%52%100%
1910267077rs2228611TC48%52%100%
1912989560rs2293682GA47%51% 
1913445208rs2248069CT100%100%46%
1916591464rs9305079GA100%50%49%
1938994910rs2229144GA  51%
202413320rs2076652TC52%100%51%
206100088rs10373AG51%45%47%
2019970705rs2076584CT100%100%51%
2035865054rs4608CT100%48%100%
2144323590rs4148973TG48%51%48%
2146908355rs11702425TC51%51%47%
2147773103rs2249057CA100%47%50%
2221141300rs4675TC51%51%48%
2237469591rs4820268GA51%100%50%

The xGen Sample ID Amplicon Panel was used with 10 ng of gDNA from different Coriell samples to create libraries. Sequencing was performed using MiSeq® V2 Reagents. SNP allele frequencies were determined using GATK HaplotypeCaller (Broad Institute). Homozygous SNPs are indicated in blue and heterozygous SNPs are indicated in green. Positions on GHCh37 (hg19). Clear differences are observed between the DNA samples, demonstrating the genotype determination possible with xGen Sample ID Amplicon Panel.

Amplicon distribution per chromosome

Amplicons per chromosome in xGen Sample ID Amplicon Panel consists of 104 amplicons, 95 of which cover known exonic SNPs, and 9 are for gender identification. This coverage gives a discrimination power of 1:85,000 [1].

Chr #amps
X 1
Y 8
1 8
2 21
3 5
4 5
5 7
6 3
7 6
8 3
9 7
10 9
11 4
12 4
13 1
14 5
15 4
16 6
17 8
18 3
19 5
20 5
21 4
22 3

References

  1. Pengelly RJ, Gibson J, Andreoletti G, et al. A SNP profiling panel for sample tracking in whole-exome sequencing studiesGenome Med. 2013;5(9):89.

*RUO—For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.

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