Processing
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 index pairs
For customers who wish to purchase the legacy rhAmpSeq™ Sample ID Panel, please contact us today.
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The xGen 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 sex. This panel is compatible with circulating, cell-free DNA (cfDNA), as well as formalin-fixed paraffin embedded (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 Sample ID Amplicon Panels have a single tube workflow that is done in as little as 2 hours.
Figure 1. xGen Sample ID Amplicon Panels have a single tube workflow that is done in as little as 2 hours. Creating an NGS library starts with multiplex PCR. Your 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
| Features | xGenTM 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 population groups and sex.
| DNA | Sex | Race/population group | % 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 population groups and sex. Libraries were sequenced on a MiniSeq® (Illumina) instrument. On-target and coverage uniformity were calculated as per base.
| Chr | POS | SNP ID | REF | ALT | Coriell NA1278 | Coriell NA00897 | Coriell NA11496 |
|---|---|---|---|---|---|---|---|
| 1 | 67861520 | rs2229546 | C | A | 100% | 52% | |
| 1 | 158582646 | rs2251969 | T | C | 100% | ||
| 1 | 167849414 | rs203849 | A | G | 50% | 100% | |
| 1 | 179520506 | rs1410592 | G | A | 100% | 53% | 100% |
| 1 | 209811886 | rs2076356 | T | G | 53% | 52% | |
| 1 | 209968684 | rs2013162 | C | A | 100% | 47% | |
| 1 | 228431095 | rs1771455 | A | G | 47% | 100% | 53% |
| 2 | 44502788 | rs3738985 | A | C | 100% | 100% | 100% |
| 2 | 49381585 | rs1394205 | C | T | 47% | ||
| 2 | 75115108 | rs10194657 | A | G | 50% | ||
| 2 | 169789016 | rs497692 | T | C | 100% | ||
| 2 | 170092395 | rs2229267 | A | G | 52% | 47% | 51% |
| 2 | 179454394 | rs1560221 | A | G | 47% | 48% | |
| 2 | 179455207 | rs2163009 | T | C | 45% | 48% | |
| 2 | 215820013 | rs10498027 | G | A | 45% | ||
| 2 | 219941063 | rs897477 | G | A | 100% | 100% | 100% |
| 2 | 227896976 | rs10203363 | C | T | 100% | 46% | |
| 3 | 4403767 | rs2819561 | A | G | 50% | 100% | 51% |
| 3 | 4712413 | rs2306875 | G | A | 48% | 52% | 45% |
| 3 | 45989044 | rs2234358 | T | G | 49% | 100% | |
| 3 | 148727133 | rs4938 | G | A | 52% | 51% | 46% |
| 4 | 5749904 | rs386594666 | T | C | 50% | 49% | |
| 4 | 86844835 | rs6824722 | A | G | 47% | ||
| 4 | 86915848 | rs10003909 | T | C | 51% | 50% | |
| 4 | 88534235 | rs2736982 | A | G | 100% | 100% | |
| 5 | 13719022 | rs30169 | T | G | 100% | 100% | 48% |
| 5 | 13829799 | rs1348689 | G | A | 50% | 50% | 100% |
| 5 | 55155402 | rs1009639 | C | T | 99% | 99% | 99% |
| 5 | 82834630 | rs309557 | T | C | 53% | 54% | |
| 5 | 135392426 | rs4669 | T | C | 48% | ||
| 5 | 138456815 | rs3088052 | T | C | 48% | 52% | 52% |
| 6 | 146755140 | rs2942 | G | A | 46% | 47% | 49% |
| 6 | 152464839 | rs2256135 | A | G | 51% | 52% | 49% |
| 7 | 34009946 | rs10265207 | C | T | 100% | 99% | |
| 7 | 48450157 | rs17548783 | T | C | 47% | 100% | |
| 7 | 50742180 | rs1800504 | C | T | 50% | 50% | 100% |
| 7 | 100804140 | rs1048303 | C | T | 52% | 100% | |
| 7 | 127250907 | rs386607686 | T | C | 46% | 100% | 100% |
| 8 | 94935937 | rs4735258 | T | C | 100% | 51% | |
| 8 | 104337096 | rs3808554 | A | G | 48% | 47% | 45% |
| 9 | 27202870 | rs386602523 | A | G | 50% | 46% | |
| 9 | 77415284 | rs7859201 | A | C | 100% | ||
| 9 | 97365642 | rs9695 | G | A | 47% | 51% | |
| 9 | 100190780 | rs1381532 | A | G | 100% | 100% | |
| 9 | 104184022 | rs4577 | G | A | 100% | ||
| 9 | 136304497 | rs3124768 | A | G | 100% | 47% | 52% |
| 10 | 69926097 | rs2673794 | T | C | 47% | 100% | |
| 10 | 73856984 | rs3312 | A | G | 45% | ||
| 10 | 78944590 | rs1131824 | G | A | 47% | 49% | 100% |
| 10 | 85972043 | rs10749482 | A | G | 51% | 47% | 46% |
| 10 | 95791763 | rs17109674 | G | A | 50% | ||
| 10 | 104596924 | rs6163 | C | A | 47% | ||
| 10 | 104814162 | rs2275271 | T | C | 46% | ||
| 10 | 105819956 | rs805701 | G | A | 100% | 100% | 100% |
| 10 | 113920465 | rs2277207 | G | A | 48% | 47% | 47% |
| 11 | 6629665 | rs1043388 | C | T | 47% | ||
| 11 | 16133413 | rs4617548 | A | G | 100% | 45% | |
| 11 | 30255185 | rs386601843 | C | T | 51% | 48% | 100% |
| 12 | 993930 | rs7300444 | C | T | |||
| 12 | 8757481 | rs2028373 | G | A | 53% | 41% | |
| 12 | 52200742 | rs60637 | C | A | 50% | 100% | 100% |
| 14 | 50769717 | rs2297995 | G | A | 100% | 100% | |
| 14 | 64637147 | rs7161192 | C | A | 47% | ||
| 14 | 74992800 | rs699374 | A | G | 51% | 45% | |
| 14 | 76045858 | rs2287016 | G | A | |||
| 15 | 34528948 | rs4577050 | G | A | 100% | 47% | 46% |
| 15 | 89401615 | rs3825994 | T | G | 100% | 48% | 100% |
| 15 | 89402596 | rs698621 | T | G | 53% | 48% | 100% |
| 16 | 68713730 | rs2296409 | G | A | 51% | 100% | 100% |
| 16 | 68713823 | rs2296408 | C | A | 49% | 100% | 100% |
| 16 | 68729785 | rs17715450 | C | A | 48% | 100% | 100% |
| 16 | 70303580 | rs2070203 | G | A | 47% | 48% | 46% |
| 16 | 70546234 | rs3762171 | G | A | 48% | 45% | 50% |
| 17 | 7192091 | rs222842 | C | T | 47% | 100% | 100% |
| 17 | 10536018 | rs2285479 | G | A | 100% | 100% | |
| 17 | 10542471 | rs2285475 | T | G | 100% | 100% | |
| 17 | 42449789 | rs5910 | G | A | 100% | 48% | |
| 17 | 71192663 | rs1052706 | G | A | 100% | 51% | 55% |
| 17 | 71192873 | rs11544800 | A | G | 100% | 53% | 52% |
| 17 | 71197748 | rs1037256 | G | A | 100% | 49% | 56% |
| 18 | 12351342 | rs11080572 | C | T | 47% | 100% | 52% |
| 18 | 47455923 | rs2298628 | C | T | 48% | 52% | 100% |
| 19 | 10267077 | rs2228611 | T | C | 48% | 52% | 100% |
| 19 | 12989560 | rs2293682 | G | A | 47% | 51% | |
| 19 | 13445208 | rs2248069 | C | T | 100% | 100% | 46% |
| 19 | 16591464 | rs9305079 | G | A | 100% | 50% | 49% |
| 19 | 38994910 | rs2229144 | G | A | 51% | ||
| 20 | 2413320 | rs2076652 | T | C | 52% | 100% | 51% |
| 20 | 6100088 | rs10373 | A | G | 51% | 45% | 47% |
| 20 | 19970705 | rs2076584 | C | T | 100% | 100% | 51% |
| 20 | 35865054 | rs4608 | C | T | 100% | 48% | 100% |
| 21 | 44323590 | rs4148973 | T | G | 48% | 51% | 48% |
| 21 | 46908355 | rs11702425 | T | C | 51% | 51% | 47% |
| 21 | 47773103 | rs2249057 | C | A | 100% | 47% | 50% |
| 22 | 21141300 | rs4675 | T | C | 51% | 51% | 48% |
| 22 | 37469591 | rs4820268 | G | A | 51% | 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 sex 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 |
Resources
References
- Pengelly RJ, Gibson J, Andreoletti G, et al. A SNP profiling panel for sample tracking in whole-exome sequencing studies. Genome Med. 2013;5(9):89.
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