Preconception Carrier Screening

Bring expanded carrier screening by NGS to your lab with CarrierSeq ECS kits

In today’s multiethnic society, some genetic disorders previously confined to specific ethnic groups may now occur at increasing frequency in broader populations. Conventional carrier screening that targets single disorders according to ancestry or family history, based on assumptions about prevalence, may not accurately reflect changing frequencies.

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New advancements and decreasing costs of genetic analysis technologies such as next-generation sequencing (NGS) are enabling carrier screening research across a broader range of disorders. This type of research enables discovery of carrier status regardless of ancestry or geographic region, with high accuracy, quick turnaround time, and low cost.

Rigorously designed specifically for expanded carrier screening (ECS) research, the Ion Torrent CarrierSeq ECS Kit for the Ion GeneStudio S5 System is an end-to-end solution that includes reagents for library preparation, template preparation, and sequencing, plus software for data analysis and reporting. With CarrierSeq ECS kits, laboratories can now perform NGS-based expanded carrier screening research in their own labs.

Key benefits

  • Increase carrier status detection rates for a broad range of inherited disorders—The rigorously designed 420-gene panel enables the analysis of 28,000 non-benign ClinVar variants for single-nucleotide variants (SNVs), insertions and deletions (indels), and copy number variants (CNVs) by NGS.
  • Consolidate stand-alone assays to improve lab efficiency—Difficult-to-detect targets due to pseudogenes, paralogues (SMN1 and SMN2 for spinal muscular atrophy), or within a locus (HBA1 and HBA2 for alpha thalassemia) are consolidated in a single NGS assay.
  • Simplify adoption and implementation in your lab with this end-to-end solution—Our optimized assay kit streamlines implementation and helps ensure reliable and consistent results by leveraging Ion AmpliSeq technology. Intuitive and customizable data analysis software quickly translates data into results and report formats you need.


Rigorously designed content and consolidated assays

Preconception Carrier Screening
CarrierSeq ECS kits enable the analysis of more than 28,000 non-benign variants from ClinVar and other annotation sources; variants include pathogenic*, likely pathogenic*, and variants of unknown significance (VUS)* in 420 genes implicated in 418 inherited disorders. The panel comprises ~14,000 amplicons that cover the entire coding sequence (CDS) regions of target genes, including intron/exon boundaries for the analysis of SNVs and CNVs across the complete exonic regions of each gene, not only the likely pathogenic variants. Four iterations of the panel design were developed and testing was conducted with >450 true positive samples** in addition to 68 synthetic variants to ensure optimum performance.

* From ClinVar and other annotation sources
** Cell lines described in this study were obtained from the NIGMS Human Genetic Cell Repository, the NHGRI Sample Repository for Human Genetic Research, and the CDC Cell and DNA Repository, all at the Coriell Institute for Medical Research.

Rigorously designed content for accurate detection of CNVs and analysis of difficult-to-call variants (such as SMN1 and SMN2 for spinal muscular atrophy or HBA1 and HBA2 for alpha thalassemia) in a single assay.

CNV detection is an essential part of genetic analysis for inherited disorders. Accurate and reproducible CNV analysis by NGS can be a significant challenge. Through expert design for increased amplicon coverage and software algorithm developments, the CarrierSeq ECS Kits enable robust and accurate CNV analysis (in addition to SNV analysis) to maximize carrier status detection. This includes detection of known carrier variants with single exon–level resolution for >30 focused genes, such as CFTR and DMD (Table 1).

CarrierSeq-ProdBulletin-Global-FHR-2-big
Figure 1. Content for increased detection rates.

Genetic variants for a number of the most severe yet prevalent disorders can be challenging to detect by NGS assays, and therefore typically require separate additional stand-alone tests for the causative genes. Our algorithms enable a single assay despite the difficulties in variant calling as a result of pseudogenes, paralogues (such as SMN1 and SMN2 for spinal muscular atrophy), or within a locus (such as HBA1 and HBA2 for alpha thalassemia).

Research area

Gene

Targeted ClinVar SNVs/indels

CNV

Alpha thalassemia HBA1/2 SC* Yes+
Beta hemoglobinopathies HBB 267 Yes+
Bloom syndrome BLM 126 Yes
Canavan disease ASPA 64 Yes
Congenital amegakaryocytic thrombocytopenia MPL 50 Yes
Cystic fibrosis CFTR 819 Yes+
Dihydrolipoamide dehydrogenase deficiency DLD 24 Yes
Duchenne/Becker muscular dystrophy DMD 634 Yes+
Familial dysautonomia IKBKAP 1515 Yes
Familial hyperinsulinism, ABCC8-related ABCC8 542 Yes
Fanconi anemia, complementation group A FANCA 87 Yes+
Fanconi anemia, complementation group C FANCC 80 Yes+
Fanconi anemia, complementation group G FANCG 18 Yes
Galactosemia GALT 276 Yes+
Gaucher disease GBA 7* Yes
Glycogen storage disease, type IA G6PC 85 Yes
Glycogen storage disease, type IB SLC37A4 36 Yes
Joubert syndrome 2 TMEM216 15 Yes
Joubert syndrome 7 RPGRIP1L 47 Yes
Maple syrup urine disease, type IA BCKDHA 60 Yes
Maple syrup urine disease, type IB BCKDHB 90 Yes
Maple syrup urine disease, type II DBT 44 Yes
Medium-chain acyl-CoA dehydrogenase deficiency ACADM 104 Yes
Mucolipidosis IV MCOLN1 41 Yes+
line myopathy, NEB-related NEB 124 Yes
Niemann-Pick disease, type A/B SMPD1 128 Yes
Phenylketonuria PAH 277 Yes+
Smith-Lemli-Opitz syndrome DHCR7 95 Yes
Spinal muscular atrophy SMN1 SC* Yes+
Tay-Sachs disease HEXA 166 Yes+
Usher syndrome, type 1F PCDH15 77 Yes+
Usher syndrome, type 3A CLRN1 23 Yes
Walker-Warburg syndrome, FKTN-related FKTN 36 Yes

Table 1. Partial CarrierSeq ECS gene list

Yes+ = enhanced amplicon design and coverage  
SC = special case genes
* Specialized algorithms are used for these special-case genes.

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Streamlined implementation and workflow

CarrierSeq ECS Kits include reagents for library preparation, template preparation, and sequencing plus software for data analysis and reporting. The reagents are optimized to work together out of the box (Figure 2).

For library preparation, CarrierSeq ECS Kits use the globally recognized, superior Ion Ampliseq technology, a fast and simple amplicon-based enrichment method for targeted NGS. The proprietary, proven Ion AmpliSeq technology combines thousands of primer pairs into a single PCR reaction for robust and consistent library preparation. Ion AmpliSeq technology has seen broad global adoption and resulted in over 1,000 peer reviewed publications across a broad range of applications including inherited disease and cancer research.

Using the Ion Chef and Ion GeneStudio S5 systems for template preparation and sequencing, and a suite of software programs for data analysis, the CarrierSeq ECS Kits offer a seamless workflow for carrier screening research.

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Library prep
Rapid preparation of amplicon libraries using Ion Torrent CarrierSeq ECS Panel based on the globally recognized Ion AmpliSeq technology.


Day 1 of the workflow
Hands-on time: 1 hr

Template prep on Ion Chef Instrument
Robust and automated template preparation with integrated sample tracking using prepackaged and ready-touse reagent cartridge


Day 1 of the workflow (overnight run)
Hands-on time: 15 min

Sequencing on Ion GeneStudio S5 System
Fast and easy-to-set up sequencing using prepackaged reagent cartridge; choice of two different Ion Chip Kits for sample throughput flexibility


Day 2 of the workflow
Hands-on time: <15 min

Data analysis
Complete data analysis workflow to quickly translate data into results, including customizable analysis and reporting options for flexible viewing

Figure 2. Streamlined 2-day workflow for fast turnaround from genomic DNA to variant calls.


Straightforward and powerful data analysis

Three software tools work together seamlessly to reduce the need for extensive bioinformatics expertise to perform various analyses and provide a concise result report with high confidence (Figure 3).

Torrent Suite Software is used for fast and easy sequencing run planning, monitoring, automated sequencing, primary data analysis, and alignment. Data are automatically exported to the Ion Reporter Software and further processed with preconfigured CarrierSeq workflows to call variants, such as SNVs, indels, and CNVs, as well as putative gene conversion events.

Lastly, the Carrier Reporter Software, a straightforward yet powerful software, is designed specifically for carrier screening research analysis and reporting. The software automatically classifies the variants based on pathogenicity according to ClinVar, proprietary databases, and the American College of Medical Genetics and Genomics (ACMG)–predicted pathogenicity guidelines. The software also enables the user to customize the variant classifications based on their own guidelines and store them in the system for use in subsequent analyses. The intuitive user interface presents the sequencing QC information and carrier results including no call information for individuals or couples. Finally, the software enables customization such that the user may analyze and report only the variants and genes of interest (for example, American College of Obstetricians and Gynecologists (ACOG)–recommended genes for common disorders).

sequencingdata

Torrent Suite Software

Plan, monitor, and track your runs all within a browser while reviewing the quality and accuracy of your sequencing run.

variantcnv

Ion Reporter Software

Identify variants such as SNVs, indels, and CNVs with preconfigured and customizable workflows, providing flexibility for users of any experience level.

variant

Carrier Reporter Software

Classify variants according to pathogenicity based on ACMG and ClinVar guidelines. Customize analysis and reporting at variant and gene levels.

Figure 3. Straightforward bioinformatics workflow.


Flexible throughput

CarrierSeq ECS Kits are available in two different sizes to accommodate laboratories with variable throughput needs. Options for 4 or 16 samples per chip (8 or 32 samples per run) for the GeneStudio S5 System provide a cost-effective solution for variable throughput demand and a streamlined path for growth in laboratories that are increasing their carrier screening research or transitioning from outsourcing to an in-house platform.


Summary

Implementing expanded carrier screening research in your own lab is now easier than ever with CarrierSeq ECS kits and Carrier Reporter Software. This NGS-based end-to-end solution, which includes rigorously designed targeted content, optimized reagents, and intuitive data analysis software tools, is ready to implement without the need for expert-level bioinformatics resources. The assay’s ability to enable the analysis of SNVs and CNVs for the evaluation of 420 genes in a single assay, combined with intuitive and customizable analysis and reporting software tools, gives you the confidence you need to provide accurate, quick, and cost-effective results.

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