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Beacon ACMG Tier 3 Female Carrier Screening Panel

Beacon ACMG Tier 3 Female Carrier Screening Panel

  • Panel Description
  • Test Description
  • CPT Codes
  • Resources

Panel Description

The Beacon ACMG Tier 3 Carrier Screening Panel is a pan-ethnic carrier screen for more than 100 autosomal recessive and X-linked conditions. This panel exclusively includes genes included in the 2021 ACMG Practice Resource for screening for autosomal recessive and X-linked conditions during pregnancy and preconception.

Our technology establishes Beacon as the most intensive carrier screening with the highest accuracy available.

  • Sequence variants and small insertions/deletions: unless otherwise specified, whole gene sequencing (coding regions and adjacent intronic/splice regions) is performed with >99% of bases covered by at least 20 independent sequence reads (“20x”). Additionally, intronic and promoter mutations specified in ClinVar and the Human Gene Mutation Database (HGMD) are targeted with >98% sensitivity.
  • Deletion/duplications (del/dup): copy number variants (also known as deletions/duplications, or del/dup for short) are detected using Fulgent’s sophisticated bioinformatic algorithm, CNVexonTM. Pathogenic variants found by this method are confirmed by Sanger sequencing, MLPA, or quantitative PCR (qPCR).
  • Fragile X: The trinucleotide repeat (CGG) expansion in the 5’ untranslated region of FMR1 is detected by repeat-primed PCR (rpPCR). Premutation carriers are sequenced by Sanger sequencing to detect AGG interruptions.
  • Spinal Muscular Atrophy: copy number changes in the SMN1 gene are screened by NGS and confirmed by MLPA. Point mutations for spinal muscular atrophy are not detected due to high sequence homology.
  • Pseudogenes: proprietary bioinformatics tools are employed to identify carrier mutations in disease genes (such as GBA for Gaucher disease and HBA1/HBA2 for alpha thalassemia) which have highly similar inactive counterparts.

Reporting options: Only variants classified as “Pathogenic” or “Likely Pathogenic” using the ACMG guidelines for sequence variant interpretation will be reported.

Detection rate: A broad range of laboratory and computational tools are employed to ensure the highest detection rate. The analytical detection rate for all genes is >98%.

*Male patients will not be screened for X-linked conditions (e.g., FMR1, etc.). If an X-linked condition is suspected in a male patient, please contact Fulgent Genetics or a genetics professional about diagnostic testing for that disorder.

Test Description

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Order Options:
  • Sequencing (included)
  • Del/Dup (included)
  • Duo/Trio
Turnaround Time:
2 weeks
Cost:
Call for details
Genes:
ABCA3, ABCC8, ABCD1, ACADM, ACADVL, ACAT1, AFF2, AGA, AGXT, AHI1, AIRE, ALDOB, ALPL, ANO10, ARSA, ARX, ASL, ASPA, ATP7B, BBS1, BBS2, BCKDHB, BLM, BTD, CBS, CC2D2A, CCDC88C, CEP290, CFTR, CHRNE, CLCN1, CLRN1, CNGB3, COL7A1, CPT2, CYP11A1, CYP21A2, CYP27A1, CYP27B1, DHCR7, DHDDS, DLD, DMD, DYNC2H1, ELP1, ERCC2, EVC2, F8, F9, FAH, FANCC, FKRP, FKTN, FMO3, FMR1, FXN, G6PC, GAA, GALT, GBA, GBE1, GJB2, GLA, GNPTAB, GRIP1, HBA1, HBA2, HBB, HEXA, HPS1, HPS3, IDUA, L1CAM, LRP2, MCCC2, MCOLN1, MCPH1, MID1, MLC1, MMACHC, MUT, MVK, NAGA, NEB, NPHS1, NR0B1, OCA2, OTC, PAH, PCDH15, PKHD1, PLP1, PMM2, POLG, PRF1, RARS2, RNASEH2B, RPGR, RS1, SCO2, SLC19A3, SLC26A2, SLC26A4, SLC37A4, SLC6A8, SMN1, SMPD1, TF, TMEM216, TNXB, TYR, USH2A, XPC ( 113 genes )
Detection Rate:
~99% @ 20x
Coverage:
98% at 20x
Specimen Requirements:
Blood (two 4ml EDTA tubes, lavender top) or Extracted DNA (3ug in EB buffer) or Buccal Swab or Saliva (kits available upon request)
Test Limitations:
All sequencing technologies have limitations. This analysis is performed by Next Generation Sequencing (NGS) and is designed to examine coding regions and splicing junctions. Although next generation sequencing technologies and our bioinformatics analysis significantly reduce the contribution of pseudogene sequences or other highly-homologous sequences, these may still occasionally interfere with the technical ability of the assay to identify pathogenic variant alleles in both sequencing and deletion/duplication analyses. Sanger sequencing is used to confirm variants with low quality scores and to meet coverage standards. If ordered, deletion/duplication analysis can identify alterations of genomic regions which include one whole gene (buccal swab specimens and whole blood specimens) and are two or more contiguous exons in size (whole blood specimens only); single exon deletions or duplications may occasionally be identified, but are not routinely detected by this test. Identified putative deletions or duplications are confirmed by an orthogonal method (qPCR or MLPA). This assay will not detect certain types of genomic alterations which may cause disease such as, but not limited to, translocations or inversions, repeat expansions (eg. trinucleotides or hexanucleotides), alterations in most regulatory regions (promoter regions) or deep intronic regions (greater than 20bp from an exon). This assay is not designed or validated for the detection of somatic mosaicism or somatic mutations.

Gene Specifics:
Gene Notes
AFF2 The current testing method does not assess trinucleotide repeat expansions in this gene. Unless otherwise specified above, only sequence variants and copy number changes in this gene are tested.
F8 The current testing method does not include detection of intron 1/intron 22 inversions in the F8 gene. This detection is available upon request.
FXN The FXN gene mutations most commonly associated with disease are expansions of a GAA trinucleotide repeat sequence. Only sequence variants and copy number changes in this gene are tested as part of this test unless specifically noted above. Repeat expansion testing may be warranted if the clinical presentation of the patient is specific for a condition associated with this gene.
CPT Codes:
CPT Code 81408, 81406

NOTE:  The CPT codes listed on the website are in accordance with Current Procedural Terminology, a publication of the American Medical Association. CPT codes are provided here for the convenience of our clients. Clients who bill for services should make the final decision on which codes to use.

Resources

  1. Carrier screening for genetic conditions. Committee Opinion No. 691. American College of Obstetricians and Gynecologists. Obstet Gynecol 2017;129:e41-55
  2. Carrier screening in the age of genomic medicine. Committee Opinion No. 690. American College of Obstetricians and Gynecologists. Obstet Gynecol 2017;129e35-40
  3. Edwards et al. Expanded Carrier Screening in Reproductive Medicine--Points to Consider. A Joint Statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine. Obstet Gynecol 2015; 125(3)
  4. Gregg AR, et al. ACMG Professional Practice and Guidelines Committee. Screening for autosomal recessive and X-linked conditions during pregnancy and preconception: a practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2021 Oct;23(10):1793-1806. PMID: 34285390.
  5. Prior TW. Carrier screening for spinal muscular atrophy. ACMG Practice Guidelines. Genet Med 2008:10(11):840-842
  6. Sherman S et al. Fragile X syndrome: Diagnostic and carrier testing. ACMG Practice Guidelines. Genet Med 2005:7(8):584-587
  7. Watson MS et al. Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel. ACMG Policy Statement. Genet Med 2004:6(5):387-391