CarrierScan-Assay

Transform carrier screening research

Advances in genetic analysis tools are revolutionizing reproductive health and transforming the way carrier screening research is being conducted. Traditionally, molecular research laboratories have focused on analyzing just a few genetic changes that cause inherited diseases and are known or assumed to be associated with an individual’s ethnicity. With the identifi cation of more causative variants—both sequence and structural—and increasing ethnic diversity in certain regions, it is becoming signifi cantly important to expand carrier screening research to include more variants and diseases.

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The Applied Biosystems CarrierScan Assay is an innovative, comprehensive, and high-throughput microarray-based tool for the reliable and robust detection of sequence and structural variation for preconception expanded carrier screening research across a wide range of ethnicities. The unique feature of this tool is the ability to consolidate multiple copy number and genotyping tests into a single molecular assay. With simple data analysis and reporting software included in the complete solution, high-throughput molecular labs can generate all relevant carrier screening research data quickly. The complete CarrierScan Assay solution offers flexibility and scalability to meet the changing needs of high-throughput molecular research labs, and includes the following components:

Reagents

Reagents for manual or automatated sample preparation

96-array plate

96-array plate

GeneTitan MC Instrument

GeneTitan MC Instrument

CarrierScan-Reporter-Software

CarrierScan Reporter Software for data analysis and export


Consolidate multiple assays into one

To perform expanded carrier screening research efficiently and reliably, a laboratory must be able to assess a wide range of genetic changes in each sample. For example, recessively inherited complex conditions (Figure 1) such as α- and β-thalassemia can be caused by multiple types of genetic variants, including copy number deletions or duplications in either HBA1, HBA2, or both genes (α-thalassemia), and mutations in the HBB gene (β-thalassemia and sickle-cell anemia). For accurate detection of each of these variants, multiple technologies including PCR, multiplex ligation-dependent probe amplification (MLPA), sequencing, and microarrays are needed for comprehensive analysis of a single sample. This extensive requirement may limit a laboratory’s potential throughput and may increase infrastructure, maintenance, and labor costs.

CarrierScan Figure 1

Figure 1. Common genetic conditions requiring detection of both sequence and structural variants.

Trust your results with verified content

All detection probes used on the CarrierScan microarray have been empirically selected based on assessment of performance in more than 1,500 samples with variants to enable highly accurate, reproducible, and robust data.

Empirical probe selection enables:

  • Reduction of false calls caused by neighboring interfering variants (e.g., the delta F508 mutation on the CFTR gene)
  • High true variant detection even in challenging regions of sequence homology in pseudogenes (e.g., GBA and ARSA, among others)

In addition, the most common variants have been technically and biologically verified at multiple independent locations using variant-positive samples—yielding 100% concordant results, and demonstrating excellent robustness and reproducibility. The CarrierScan Assay also offers the flexibility to analyze multiple sample types, including whole blood, tissue, cell lines, and buccal samples with a >98% pass rate.


Comprehensive coverage from the content sources you trust

The CarrierScan Assay detects approximately 6,000 sequence and structural variants in over 600 genes for 600 diseases, informed by the American College of Medical Genetics (ACMG) and the American College of Obstetricians and Gynecologists (ACOG) guidelines from well-curated, prominent databases and peer-reviewed literature [1–6]. Figure 2 shows examples of the comprehensive content offered by the CarrierScan Assay. For the CFTR gene, as an example, detection probes are included only for those mutations that are found in databases and for which relevance has been confirmed in published literature. Additionally, exon-level copy number markers are included to increase the sensitivity of the assay. Likewise, for the DMD gene, exon-level coverage is achieved with more than 12,000 empirically selected probes for reliable detection of structural variants containing deletions and duplications (del/dups). The comprehensive content also includes optional ancestry-informative markers (AIMs) for population analysis, and probes for sample identity tracking and quality assurance.

CarrierScan Figure 2

Figure 2. Examples of the comprehensive content included in the CarrierScan Assay.


Simple data analysis and reporting

Powerful biallelic and multiallelic detection, as well as state-of-the-art copy number algorithms are included in CarrierScan Reporter Software and used in conjunction with curated annotations for population frequencies, providing quick, reliable, and automated data analysis. CarrierScan Reporter Software automates the most common calculations for single and paired sample analysis for carrier screening research, making reporting simple. Export of annotations is customizable by population or panel, allowing you to filter and translate data quickly and easily into a format that meets your specific laboratory needs (Figure 3). Additionally, due to the intrinsic complexity of the SMN1 gene (spinal muscular atrophy), the included SMN Reporter Software discerns carrier states for SMN1. It provides reliable SMN1 calls, generates plots for each sample, and provides a single carrier status call that can be easily exported into a report. The combined softwares help you analyze and report data with ease.

Figure 3. Data analysis workfl ow steps in CarrierScan Reporter Software.

Disorder Gene Variants detected
  Sequence Structural
Hyperinsulinemic hypoglycemia, familial, 1
ABCC8
82  
Canavan disease
ASPA
48
 
Maple syruurine disease, type IA
BCKDHA
24
 
Maple syruurine disease, type IB
BCKDHB
32
 
Maple syruurine disease, type II
DBT
9
Yes
Bloom syndrome
BLM
54
 
Cystic fibrosis
CFTR
661
Yes
Usher syndrome, type 3A
CLRN1
4
 
Dihydrolipoamide dehydrogenase deficiency
DLD
10
 
Fanconi anemia, complementation grou A
FANCA
21
Yes
Fanconi anemia, complementation group C FANCC
30
 
Fanconi anemia, complementation grou G
FANCG
9
 
Fukutin
FKTN
10
 
Glycogen storage disease type IA
G6PC
71
 
Glycogen storage disease type IB
SLC37A4<> 16
 
Gaucher disease
GBA
30
 
α-Thalassemia
HBA1/HBA2
12
Yes
Sickle-cell disorders and β-thalassemia
HBB
126
Yes
Tay-Sachs disease
HEXA
85
Yes
Familial dysautonomia
IKBKAP
3
 
Mucolipidosis IV
MCOLN1
15
Yes
Myeloproliferative leukemia virus oncogene
MPL
11
 
Nebulin
NEB
7
Yes
Protocadherin-related 15
PCDH15
9
 
Niemann-Pick disease, type A/B
SMPD1
52
 
Joubert syndrome 2
TMEM216
7
 
Joubert syndrome 7
RPGRIP1L
2
 
Spinal muscular atrophy
SMN1
11
Yes

References

  1. Grody WW et al. (2013) ACMG position statement on prenatal/preconception expanded carrier screening. Genet Med 15:482–483.2. 
  2. Landrum MJ et al. (2016) ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res 44:D862–868.3. 
  3. Stenson PD et al. (2003) Human Gene Mutation Database (HGMD): 2003 update. Hum Mutat 21:577–581.4. 
  4. Zlotogora J et al. (2015) The Israeli national population program of genetic carrier screening for reproductive purposes. Genet Med 18:203–206.5. 
  5. Langfelder-Schwind E et al. (2014) Molecular testing for cystic fibrosis carrier status practice guidelines: recommendations of the National Society of Genetic Counselors. J Genet Couns 23:5–15.6. 
  6. Sosnay PR et al. (2013) Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet 45:1160–1167.