Test Code: 1153

ACOG/ACMG Carrier Screen: Targeted Mutation Panel
Test Code: 1153
Turnaround time: 3 weeks

CONDITION DESCRIPTION
Test components:

  • Carrier screening for cystic fibrosis as recommended by the American College of Medical Genetics (ACMG) and the American Congress of Obstetricians and Gynecologists (ACOG)
  • Carrier screening for four conditions (Tay-Sachs, Canavan disease, cystic fibrosis, and familial dysautonomia) common to those of Ashkenazi Jewish descent, as recommended by ACOG, and five additional conditions (Bloom syndrome, Fanconi anemia type C, Gaucher disease, Niemann-Pick type A, and Mucolipidosis IV), as recommended by ACMG
  • Carrier screening for spinal muscular atrophy (SMA) as recommended by ACMG

With the utilization of next generation sequencing, carrier screening panels have been expanding to cover more and more conditions over the last five years. Although 47% of physicians note patients requesting this expanded testing, 37% of physicians prefer to only offer testing recommended by the professional societies (Ref 1). To address this need, the ACOG/ACMG Carrier Screen was developed. This screen only incorporates conditions specifically recommended by at least one of these societies.

This panel is available as full gene sequencing or targeted mutation analysis. CEN4GEN also offers single-gene sequencing for all genes on the panel, which may be utilized to more completely screen partners of positive carriers.

Although a positive test result should not affect the health of the individual, she could be at a 25% risk for passing that condition on to her children depending on the carrier status of the partner. In addition to the specific pathogenic variants identified by the panel, CEN4GEN also offers single- gene, full gene sequencing for genes on the panel, which can be utilized to screen partners of positive carriers. Knowing about these risks ahead of time can help couples make decisions about testing options prior to and during pregnancy, and can help healthcare providers be more readily prepared to offer appropriate follow-up care at delivery.

Please note that ACMG is not opposed to expanded carrier screening as long as the clinical implications of the condition and mutations are known, adult-onset and mild or incompletely penetrant diseases are limited, meaningful risks can be calculated, and proper consent is available (Ref 2).

 

ConditionGeneMutations
Bloom SyndromeBLM2281del6ins7*, 2407insT, Q645X, Q700X, R899X
Canavan DiseaseASPA433-2A>G, Y231X*, A305E, E285A*
Cystic FibrosisCFTR142 mutation panel including 23 ACMG recommended mutations (see below)
Familial DysautonomiaIKBKAP2204+6T>C, R696P*
Fanconi Anemia Type CFANCC322delG, IVS4+4A>T*, R548X, Q13X, R185X, L554P
Gaucher Disease Type 1GBA84GG*, del55bp, IVS2+1G>A*, D409H, D409V, L444P*, N370S*, R463C, R463H, R496H, V394L
Mucolipidosis Type IVMCOLN1Exon1 - Exon7del (Del6.4kb)*, IVS3-2A>G*
Niemann-Pick Type ASMPD1fsP330*, R610del, H423Y, L302P*,R476W, R496L*, T324I
Spinal Muscular AtrophySMN1Gene dosage
Tay-Sachs DiseaseHEXA1278insTATC*, del7.6kb, 1421+1G>C*, IVS7+1G>A, IVS9+1G>A, E462V, G250D, G269S*, R170W, R178H, R247W, R249W

*Testing for these mutations is recommended by the American College of Medical Genetics (ACMG). Genet Med 2008:10(1):54-56.

References:
1. Benn P, Chapman AR, Erickson K, et al. Obstetricians and gynecologists’ practice and opinions of expanded carrier testing and noninvasive prenatal testing. Prenat Diagn. 2014 Feb;34(2):145-52.
2. Grody WW, Thompson BH, Gregg AR, et al. ACMG position statement on prenatal/preconception expanded carrier screening. Genet Med. 2013 Jun;15(6):482-3.

GENES
ASPA,BLM,CFTR,FANCC,GBA,HEXA,IKBKAP,MCOLN1,SMN1,SMPD1

INDICATIONS
This test is indicated for:

  • Individuals or couples seeking to assess reproductive risk for a variety of conditions.
  • Individuals or couples of high-risk ethnic groups or backgrounds.

METHODOLOGY

Next Generation Sequencing: Targeted mutation analysis: In solution hybridization followed by next generation sequencing at a mean read depth of >200X of the targeted mutation regions including large indels was performed on this individual’s genomic DNA. If the targeted mutation region has a pseudogene, gene specific PCR and sequence analysis was performed by Sanger sequencing. Nucleotide numbering is based on GenBank accession numbers given in the report; nucleotide 1 corresponds to the A of the start codon ATG.

Spinal Muscular Atrophy (SMA) Testing: SMN1 gene deletions were quantified by multiplex ligation polymerase chain reaction amplification (MLPA) of exons 7 and 8. Gene dosage ratios of SMN1 are calculated relative to the average of 16 reference loci and are expressed as gene dosage, and/or copy number. Diploid gene dose or 2 copies of SMN1 indicates normal (not affected) status, 1x gene dosage or 1 copy of the SMN1 gene most likely indicates carrier status and deletions (less than 0.1x) of SMN1 or 0 copies of the SMN1 gene designates affected status. This carrier assay tests for the common SMN1 deletion only; other pathogenic variants will not be detected. SMN2 copy number is not assessed.

DETECTION

Next Generation Sequencing: Clinical Sensitivity: See results report. Pathogenic variants in regions other than the targeted area, including the promoter region, some mutations in the introns and other regulatory element mutations, cannot be detected by this analysis. Large deletions/duplications will not be detected by this analysis. Results of molecular analysis should be interpreted in the context of the patient’s clinical/biochemical phenotype.

For Spinal Muscular Atrophy (SMA) Testing: Deletions of the SMN1 gene are found in approximately 95% of individuals with SMA. This carrier assay tests for the common SMN1 deletion only; other pathogenic variants will not be detected. SMN2 copy number is not assessed.

SPECIMEN REQUIREMENTS

Submit only 1 of the following specimen types

Type: Saliva
Specimen Requirements: OrageneTM Saliva Collection Kit.

Specimen Collection and Shipping: Store sample at room temperature. Ship sample within 5 days of collection at room temperature with overnight delivery.

Type: Whole Blood
Specimen Requirements: In EDTA (purple top) tube: Infants (2 years): 3-5 ml
Older Children & Adults: 5-10 ml.

Specimen Collection and Shipping: Ship sample at room temperature with overnight delivery.

Type: Isolated DNA
Specimen Requirements: In microtainer: 60 μg
Isolation using the QiagenTM Puregene kit for DNA extraction is recommended.

Specimen Collection and Shipping: Refrigerate until time of shipment in 100 ng/ul of TE buffer. Ship sample at room temperature with overnight delivery.

RELATED TESTS

  • ACOG/ACMG Carrier Screen: Gene Sequencing Panel
  • Pan-Ethnic Carrier Screen: Targeted Mutation Panel
  • Ashkenazi Jewish Carrier Screen: Targeted Mutation Panel