Inheritest® Carrier Screen, Comprehensive Panel (144 Genes)

Inheritest® Comprehensive Panel, NGS

CPT: 81243; 81329; 81443
Updated on 2/12/2019
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Test Details

Synonyms

  • Pan-ethnic Carrier Screening

Test Includes

Screening for 144 genes, including fragile X carrier screening and spinal muscular atrophy (SMA) carrier screening. This test includes: ABCC8, ACADM, ADA, AGA, AGL, AGXT, ALDH3A2, ALDOB, ARSA, ASL, ASPA, ASS1, ATM, ATP7B, BBS1, BBS10, BCKDHA, BCKDHB, BCS1L, BLM, CBS, CFTR, CLN3, CLN5, CLN8, CLRN1, CTNS, DHCR7, DLD, DMD, DPYD, ETHE1, FAH, FANCC, FKTN, G6PC, GAA, GALC, GALT, GBA, GCDH, GLDC, GRHPR, GSS, HADHA, HBA1, HBA2, HBB, HEXA, HEXB, HLCS, HMGCL, HSD17B4, IDUA, IKBKAP, LAMA3, LAMB3, LAMC2, LRPPRC, MAN2B1, MCOLN1, MEFV, MMAA, MMAB, MMACHC, MUT, NBN, NEB, NPC1, NPC2, NPHS1, NPHS2, PAH, PCCA, PCCB, PCDH15, PEX1, PEX7, PKHD1, PMM2, PPT1, RMRP, SACS, SLC12A6, SLC17A5, SLC26A2, SLC37A4, SMPD1, TMEM216, TPP1, ACADVL, ACAT1, ADAMTS2, ALPL, AMT, ARSB, BBS2, COL4A3, COX15, CPS1, CPT2, CTSA, DHDDS, ERCC5, FMR1, FOXRED1, FUCA1, GALNS, GAMT, GLB1, GNPTAB, GNS, GUSB, HGSNAT, IDS, IL2RG, MANBA, MPL, MTTP, NAGLU, NDUFAF2, NDUFS4, NDUFS7, NDUFV1, NEU1, OTC, PDHA1, PEX10, PEX12, PEX2, PEX26, PEX6, PHGDH, SGSH, SLC22A5, SLC25A20, SLC35A3, SMN1, SUMF1, SURF1, TTPA, VPS13B, XPA and XPC.

Screening for 141 genes, including fragile X carrier screening and spinal muscular atrophy (SMA) carrier screening. This test includes: ABCC8, ACADM, ADA, AGA, AGL, AGXT, ALDH3A2, ALDOB, ARSA, ASL, ASPA, ASS1, ATM, ATP7B, BBS1, BBS10, BCKDHA, BCKDHB, BCS1L, BLM, CBS, CFTR, CLN3, CLN5, CLN8, CLRN1, CTNS, DHCR7, DLD, DPYD, ETHE1, FAH, FANCC, FKTN, G6PC, GAA, GALC, GALT, GBA, GCDH, GLDC, GRHPR, GSS, HADHA, HBB, HEXA, HEXB, HLCS, HMGCL, HSD17B4, IDUA, IKBKAP, LAMA3, LAMB3, LAMC2, LRPPRC, MAN2B1, MCOLN1, MEFV, MMAA, MMAB, MMACHC, MUT, NBN, NEB, NPC1, NPC2, NPHS1, NPHS2, PAH, PCCA, PCCB, PCDH15, PEX1, PEX7, PKHD1, PMM2, PPT1, RMRP, SACS, SLC12A6, SLC17A5, SLC26A2, SLC37A4, SMPD1, TMEM216, TPP1, ACADVL, ACAT1, ADAMTS2, ALPL, AMT, ARSB, BBS2, COL4A3, COX15, CPS1, CPT2, CTSA, DHDDS, ERCC5, FMR1, FOXRED1, FUCA1, GALNS, GAMT, GLB1, GNPTAB, GNS, GUSB, HGSNAT, IDS, IL2RG, MANBA, MPL, MTTP, NAGLU, NDUFAF2, NDUFS4, NDUFS7, NDUFV1, NEU1, OTC, PDHA1, PEX10, PEX12, PEX2, PEX26, PEX6, PHGDH, SGSH, SLC22A5, SLC25A20, SLC35A3, SMN1, SUMF1, SURF1, TTPA, VPS13B, XPA and XPC.

Screening for 144 genes, including fragile X carrier screening and spinal muscular atrophy (SMA) carrier screening. This test includes: ABCC8, ACADM, ADA, AGA, AGL, AGXT, ALDH3A2, ALDOB, ARSA, ASL, ASPA, ASS1, ATM, ATP7B, BBS1, BBS10, BCKDHA, BCKDHB, BCS1L, BLM, CBS, CFTR, CLN3, CLN5, CLN8, CLRN1, CTNS, DHCR7, DLD, DMD, DPYD, ETHE1, FAH, FANCC, FKTN, G6PC, GAA, GALC, GALT, GBA, GCDH, GLDC, GRHPR, GSS, HADHA, HBA1, HBA2, HBB, HEXA, HEXB, HLCS, HMGCL, HSD17B4, IDUA, IKBKAP, LAMA3, LAMB3, LAMC2, LRPPRC, MAN2B1, MCOLN1, MEFV, MMAA, MMAB, MMACHC, MUT, NBN, NEB, NPC1, NPC2, NPHS1, NPHS2, PAH, PCCA, PCCB, PCDH15, PEX1, PEX7, PKHD1, PMM2, PPT1, RMRP, SACS, SLC12A6, SLC17A5, SLC26A2, SLC37A4, SMPD1, TMEM216, TPP1, ACADVL, ACAT1, ADAMTS2, ALPL, AMT, ARSB, BBS2, COL4A3, COX15, CPS1, CPT2, CTSA, DHDDS, ERCC5, FMR1, FOXRED1, FUCA1, GALNS, GAMT, GLB1, GNPTAB, GNS, GUSB, HGSNAT, IDS, IL2RG, MANBA, MPL, MTTP, NAGLU, NDUFAF2, NDUFS4, NDUFS7, NDUFV1, NEU1, OTC, PDHA1, PEX10, PEX12, PEX2, PEX26, PEX6, PHGDH, SGSH, SLC22A5, SLC25A20, SLC35A3, SMN1, SUMF1, SURF1, TTPA, VPS13B, XPA and XPC.

Use

Carrier testing by analyzing 144 genes for more than 9,400 pathogenic variants associated with more than 116 autosomal recessive or X-linked disorders, including fragile X syndrome and spinal muscular atrophy.

Carrier screening for more than 7,400 mutations in 141 genes associated with more than 114 different inherited diseases, including fragile X syndrome and spinal muscular atrophy

Carrier testing by analyzing 144 genes for more than 9,400 pathogenic variants associated with more than 116 autosomal recessive or X-linked disorders, including fragile X syndrome and spinal muscular atrophy.

Limitations

Technologies used do not detect germline mosaicism and do not rule out the presence of large chromosomal aberrations, including rearrangements, or variants in regions or genes not included in this test, or possible inter/intragenic interactions between variants. In-frame and out-of-frame deletions in the DMD gene cannot be distinguished by this analysis, which does not determine precise breakpoints. A deletion or duplication of exons in the DMD gene is identified when more than >60% of an exon has an aberrant copy number. Variant classification and/or interpretation may change over time if more information becomes available. False positive or false negative results may occur for reasons that include: rare genetic variants, sex chromosome abnormalities, pseudogene interference, blood transfusions, bone marrow transplantation, somatic or tissue-specific mosaicism, mislabeled samples, or erroneous representation of family relationships.

This test was developed and its performance characteristics determined by Esoterix Genetic Laboratories LLC. It has not been cleared or approved by the Food and Drug Administration.

Variants known to be benign and synonymous variants not previously recorded in our internal variant database are not reported. This analysis does not detect germline mosaicism, and does not rule out the presence of large chromosomal aberrations including deletions, insertions, and rearrangements, or mutations in regions or genes not included in this test, and possible inter/intragenic interactions between sequence variants. False-positive or false-negative results may occur for reasons that include genetic variants, blood transfusions, bone marrow transplantation, mislabeling of samples, or erroneous representation of family relationships.

This test was developed, and its performance characteristics determined, by Esoterix Genetic Laboratories LLC. It has not been cleared or approved by the US Food and Drug Administration (FDA).

Technologies used do not detect germline mosaicism and do not rule out the presence of large chromosomal aberrations, including rearrangements, or variants in regions or genes not included in this test, or possible inter/intragenic interactions between variants. In-frame and out-of-frame deletions in the DMD gene cannot be distinguished by this analysis, which does not determine precise breakpoints. A deletion or duplication of exons in the DMD gene is identified when more than >60% of an exon has an aberrant copy number. Variant classification and/or interpretation may change over time if more information becomes available. False positive or false negative results may occur for reasons that include: rare genetic variants, sex chromosome abnormalities, pseudogene interference, blood transfusions, bone marrow transplantation, somatic or tissue-specific mosaicism, mislabeled samples, or erroneous representation of family relationships.

This test was developed and its performance characteristics determined by Esoterix Genetic Laboratories LLC. It has not been cleared or approved by the Food and Drug Administration.

Methodology

Next generation sequencing (NGS): Genomic regions of interest are selected using the Agilent®SureSelectXT® hybridization capture method for target enrichment and sequenced via the Illumina® next generation sequencing platform. Sequencing reads are aligned with the human genome reference GRCh37/hg19 build. Targeted regions are sequenced to at least 200X mean base coverage with a minimum of 99% of bases at ≥20X coverage. Analytical sensitivity is estimated to be >99% for single nucleotide variants and small insertions/deletions (<5 bp).

Alpha‐thalassemia: Analysis of the alpha‐globin (HBA) gene cluster is performed by multiplex ligationdependent amplification (MLPA). Variants included in the analysis are the Constant Spring non‐deletion variant and the following deletions: ‐alpha3.7, ‐alpha4.2, ‐alpha20.5, ‐‐SEA, ‐‐FIL, ‐‐THAI, ‐‐MED, and the HS‐40 regulatory region. This MLPA analysis does not detect other variants in the alpha‐globin genes or variants in the beta‐globin gene and may not detect the co‐occurrence of a deletion and a duplication. Analytical sensitivity is estimated to be >99% for the targeted variants.

Spinal muscular atrophy: DNA is amplified by real‐time polymerase chain reaction (PCR). The number of copies of exon 7 of SMN1 is assessed relative to internal standard reference genes. A mathematical algorithm calculates 0, 1, 2 and 3 copies with statistical confidence. If one copy of SMN1 is detected, primer and probe binding sites are sequenced to rule out variants that could interfere with copy number analysis. If no copies of SMN1 are detected, SMN2 copy number is assessed by digital PCR analysis relative to an internal standard reference gene. Copy number analysis cannot detect carriers with either 2 or, very rarely, 3 copies of SMN1 on one chromosome and no copies of SMN1 on the other chromosome.

Fragile X syndrome: DNA is amplified by the polymerase chain reaction (PCR) to determine the size of the CGG repeat within the FMR1 gene. PCR products are generated using a fluorescence labeled primer and sized by capillary gel electrophoresis. If indicated, Southern blot analysis is performed by hybridizing the probe StB12.3 to EcoRI‐ and EagI‐digested DNA. The analytical sensitivity of both Southern blot and PCR analyses is 99% for expansion mutations in the FMR1 gene. Reported CGG repeat sizes may vary as follows: +/‐ one for repeats less than 60, and +/‐ two to four for repeats in the 60 ‐ 120 range. For repeats greater than 120, the accuracy is +/‐ 10%.

Pathogenic and likely pathogenic variants are reported after confirmation by Sanger sequencing or an appropriate technology. Non‐deletion variants are specified using the numbering and nomenclature recommended by the Human Genome Variation Society (HGVS, http://www.hgvs.org/). Variants of uncertain significance and benign variants are not reported. Variant classification is consistent with ACMG standards and guidelines.1 Detailed variant classification information is available upon request.

Mutation analysis is performed using the Agilent® SureSelect® XT enrichment method and Illumina® next generation sequencing (NGS) platform. Regions of interest include all exons and splice junctions for each gene. Sequencing reads are aligned with the hg19 build of the human genome reference sequence. Analytical sensitivity is based on the depth of coverage across the regions of interest and is provided separately for each gene. Greater than 98% of target bases are covered at greater than or equal to 20x coverage. Sanger sequencing is used to confirm mutation identity and analyze regions with low coverage. Variants are reported using numbering and nomenclature recommended by the Human Genome Variation Society (HGVS) SureSelect® is a registered trademark of Agilent Technologies. Agilent® is a registered trademark of Agilent Technologies. Illumina® is a registered trademark and registered service mark of Illumina Inc.

Next generation sequencing (NGS): Genomic regions of interest are selected using the Agilent®SureSelectXT® hybridization capture method for target enrichment and sequenced via the Illumina® next generation sequencing platform. Sequencing reads are aligned with the human genome reference GRCh37/hg19 build. Targeted regions are sequenced to at least 200X mean base coverage with a minimum of 99% of bases at ≥20X coverage. Analytical sensitivity is estimated to be >99% for single nucleotide variants and small insertions/deletions (<5 bp).

Alpha‐thalassemia: Analysis of the alpha‐globin (HBA) gene cluster is performed by multiplex ligationdependent amplification (MLPA). Variants included in the analysis are the Constant Spring non‐deletion variant and the following deletions: ‐alpha3.7, ‐alpha4.2, ‐alpha20.5, ‐‐SEA, ‐‐FIL, ‐‐THAI, ‐‐MED, and the HS‐40 regulatory region. This MLPA analysis does not detect other variants in the alpha‐globin genes or variants in the beta‐globin gene and may not detect the co‐occurrence of a deletion and a duplication. Analytical sensitivity is estimated to be >99% for the targeted variants.

Spinal muscular atrophy: DNA is amplified by real‐time polymerase chain reaction (PCR). The number of copies of exon 7 of SMN1 is assessed relative to internal standard reference genes. A mathematical algorithm calculates 0, 1, 2 and 3 copies with statistical confidence. If one copy of SMN1 is detected, primer and probe binding sites are sequenced to rule out variants that could interfere with copy number analysis. If no copies of SMN1 are detected, SMN2 copy number is assessed by digital PCR analysis relative to an internal standard reference gene. Copy number analysis cannot detect carriers with either 2 or, very rarely, 3 copies of SMN1 on one chromosome and no copies of SMN1 on the other chromosome.

Fragile X syndrome: DNA is amplified by the polymerase chain reaction (PCR) to determine the size of the CGG repeat within the FMR1 gene. PCR products are generated using a fluorescence labeled primer and sized by capillary gel electrophoresis. If indicated, Southern blot analysis is performed by hybridizing the probe StB12.3 to EcoRI‐ and EagI‐digested DNA. The analytical sensitivity of both Southern blot and PCR analyses is 99% for expansion mutations in the FMR1 gene. Reported CGG repeat sizes may vary as follows: +/‐ one for repeats less than 60, and +/‐ two to four for repeats in the 60 ‐ 120 range. For repeats greater than 120, the accuracy is +/‐ 10%.

Pathogenic and likely pathogenic variants are reported after confirmation by Sanger sequencing or an appropriate technology. Non‐deletion variants are specified using the numbering and nomenclature recommended by the Human Genome Variation Society (HGVS, http://www.hgvs.org/). Variants of uncertain significance and benign variants are not reported. Variant classification is consistent with ACMG standards and guidelines.1 Detailed variant classification information is available upon request.

Specimen Requirements

Specimen

Whole blood

Volume

10 mL

Container

Yellow-top (ACD-A) tube (preferred) or lavender-top (EDTA) tube; yellow-top (ACD-B) tube is not acceptable

Storage Instructions

Maintain specimen at room temperature or refrigerate at 4°C.

Causes for Rejection

Frozen specimen; hemolysis; quantity not sufficient for analysis; improper container; blood specimens more than four days post draw

Clinical Information

Special Instructions

Test orders must include an attestation that the provider has the patient's informed consent for genetic testing. See sample physician office consent form: Consent for Genetic Testing. Call Integrated Genetics at 855-422-2557 to obtain access to genetic counseling.

Footnotes

1. Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-424.25741868
1. Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-424.25741868

LOINC® Map

Order Code Order Code Name Order Loinc Result Code Result Code Name UofM Result LOINC
451950 Inheritest Comprehensive 451999 Genetic Counselor: NGS Inheri N/A
451950 Inheritest Comprehensive 451997 Specimen Type: InheriTest 31208-2
451950 Inheritest Comprehensive 451998 Ethnicity: InheriTest 42784-9
451950 Inheritest Comprehensive 451618 Indication: 42349-1
451950 Inheritest Comprehensive 451845 Comprehensive Result: 53039-4
451950 Inheritest Comprehensive 451613 General Comments: N/A
451950 Inheritest Comprehensive 451616 Additional Clinical Info 55752-0
451950 Inheritest Comprehensive 451384 Comments: 77202-0
451950 Inheritest Comprehensive 451386 Method/Limitations: 49549-9
451950 Inheritest Comprehensive 451614 Information Table 36908-2
451950 Inheritest Comprehensive 451333 Disclaimer: N/A
451950 Inheritest Comprehensive 451612 Director Review: 72486-4
451950 Inheritest Comprehensive 451743 PDF 51969-4

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