Invitae Myelodysplastic Syndrome/Leukemia Panel

Ordering
  • Test code: 01411
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top tube
  • Alternate specimens:
    DNA or saliva/assisted saliva
  • Sample requirements
  • Request a sample kit
Billing

Test description

This test analyzes up to 21 genes that are associated with a hereditary predisposition to the development of myelodysplastic syndrome (MDS) and acute leukemias. These genes were selected based on the available evidence to date to provide Invitae’s most comprehensive hereditary MDS/leukemia panel. Some of these genes are also associated with an increased risk of other cancer types.

Genetic testing of these genes may confirm a diagnosis and help guide treatment and management decisions. Identification of a disease-causing variant would also guide testing and diagnosis of at-risk relatives. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.

If the patient has undergone a bone marrow transplant prior to genetic testing or currently has a hematological malignancy with actively circulating tumor cells, testing a sample type not derived from blood (such as skin biopsy) is warranted. While we do not accept this sample type directly, we can accept gDNA derived from skin or muscle, though deletion/duplication analysis is not guaranteed for gDNA samples because the success rate varies based on sample quality. Please see our Sample requirements page for more details.

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Primary panel (16 genes)

ATM BLM CEBPA EPCAM GATA2 HRAS MLH1 MSH2 MSH6 NBN NF1 PMS2 RUNX1 TERC TERT TP53

EPCAM: Analysis is limited to deletion/duplication analysis
MLH1: Deletion/duplication analysis covers the promoter region.
MSH2: Analysis includes the exon 1-7 inversion (Boland mutation).
TP53: Deletion/duplication analysis covers the promoter region.

Add-on preliminary-evidence genes (5 genes)

Preliminary-evidence genes currently have early evidence of a clinical association with the specific disease covered by this test. Some clinicians may wish to include genes which do not currently have a definitive clinical association, but which may prove to be clinically significant in the future. These genes can be added at no additional charge. Visit our Preliminary-evidence genes page to learn more.

BRCA1 BRCA2 BRIP1 CHEK2 PALB2

Add-on dyskeratosis congenita genes (7 genes)

Dyskeratosis congenita is a clinically and genetically heterogeneous condition that is characterized by abnormal skin pigmentation, nail dystrophy, oral leukoplakia, and increased risk of progressive bone marrow failure and development of hematologic malignancies. Additional genes associated with dyskeratosis congenita may be added to this panel at no additional charge for patients with dyskeratosis congenita-associated features.

CTC1 DKC1 NHP2 NOP10 TERC TERT TINF2

Add-on Fanconi anemia genes (17 genes)

Fanconi anemia is a multisystemic disorder that is characterized by a variable spectrum of physical abnormalities, developmental delay, and increased risk of progressive bone marrow failure and hematologic malignancy development. Additional genes associated with Fanconi anemia may be added to this panel at no additional charge for patients with Fanconi anemia-associated features.

BRCA2 BRIP1 ERCC4 FANCA FANCB FANCC FANCD2 FANCE FANCF FANCG FANCI FANCL FANCM PALB2 RAD51C SLX4 XRCC2

FANCD2: Deletion/duplication analysis is not offered for exons 14-17.

  • ataxia-telangiectasia (A-T)
  • Bloom syndrome
  • constitutional mismatch repair deficiency syndrome (CMMR-D)
  • Costello syndrome
  • familial acute myeloid leukemia (AML) with mutated CEBPA
  • familial platelet disorder with propensity to myeloid malignancy (FPD/AML)
  • GATA2 deficiency
  • Li-Fraumeni syndrome (LFS)
  • neurofibromatosis type 1 (NF1)
  • Nijmegen breakage syndrome (NBS)
  • TERT-related dyskeratosis congenita
  • TERC-related dyskeratosis congenita

MDS is a clonal hematologic disorder with ineffective production of blood cells, often characterized by cytopenias, myelodysplasia, and an increased risk of developing acute myeloid leukemia (AML). AML is characterized by the uncontrolled growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells. MDS and AML generally occur in the elderly population and the incidence increases with age. Cases of early onset MDS/AML in children or young adults may be associated with underlying genetic predisposition syndromes. Hereditary MDS or AML may present as part of the spectrum in a particular genetic syndrome with other prominent clinical features. Non-syndromic pure familial MDS/AML is characterized by a strong family history of MDS or AML without other apparent phenotypic features. Interestingly, most cases are caused by inheriting a single pathogenic variant in a gene encoding a transcription factor critical for hematopoiesis. Familial occurrences of MDS/AML appear to be rare, but they may be underdiagnosed.

Determination of an underlying genetic predisposition in an individual with a personal or family history of MDS/leukemia is critical for the selection of therapy regimens, consideration of bone marrow or stem cell transplant, long-term cancer surveillance and prognosis, and counseling of the individual and their family.

Individuals with pathogenic variants in one of these genes have an increased risk of malignancy compared to the average person, but not everyone with such a variant will actually develop cancer. Further, the same variant can present differently, even among individuals within the same family. For gene-associated cancer risks, see the table below.

Non-syndromic familial MDS/leukemia is characterized by a strong family history of MDS or leukemia without other apparent phenotypic features.

GeneEstimated MDS/leukemia riskReferences (PMIDs)
CEBPA ~90% (based on small studies) 26162409
GATA2 50%–90% 24227816, 24345756
RUNX1 ~35% (based on small studies) 18723428
TERC 30% 20507306, 19282459
TERT 30% 20507306, 19282459

Several hereditary cancer syndromes are associated with malignancies throughout childhood and into adulthood. The following genetic syndromes have been reported to increase the risk of developing leukemia, among other prominent clinical features.

ConditionGenesEstimated leukemia riskReferences (PMIDs)
Ataxia-telangiectasia ATM 70 times greater than the general population risk for acute lymphoblastic leukemia (ALL) 3459930, 12673804
Bloom syndrome BLM 15% 9062585
Constitutional mismatch repair deficiency syndrome (CMMR-D) EPCAM, MLH1, MSH2, MSH6, PMS2 elevated 18709565, 16341812, 24737826
Costello syndrome HRAS elevated 25742478, 21500339
Nijmegen breakage syndrome NBN elevated 11325820, 16840438
Neurofibromatosis type 1 NF1 11% for myelodysplastic syndrome (MDS), 200-500 times greater than the general population risk for juvenile myelomonocytic leukemia (JMML) 22240541, 23257896
Li-Fraumeni syndrome TP53 1%–3% 19204208, 20522432

The following genes confer an increased risk of MDS/leukemia in an autosomal dominant inheritance pattern:
CEBPA, GATA2, HRAS, NF1, RUNX1, TERC, TERT, TP53

The following genes confer an increased risk of MDS/leukemia in an autosomal recessive inheritance pattern:
ATM (ataxia telangiectasia), BLM (Bloom syndrome), EPCAM, MLH1, MSH2, MSH6, PMS2 (CMMR-D), and NBN (Nijmegen breakage syndrome).

This panel may be considered for individuals whose personal and/or family history is suggestive of a hereditary predisposition to MDS or leukemia, including any of the following:

  • MDS or leukemia occurring at a young age (without prior history of chemotherapy)
  • a personal or family history of:
    • low blood counts
    • bleeding diathesis
    • lymphedema
    • immune deficiencies or atypical infections
  • a family history of:
    • MDS/AML/ALL/aplastic anemia
    • early onset cancers of any type
    • several close relatives with cancer
  • additional features that are consistent with the clinical presentation of a genetic syndrome with increased risk of MDS and/or leukemia

If the patient has undergone a bone marrow transplant prior to genetic testing or currently has a hematological malignancy with actively circulating tumor cells, testing a sample type not derived from blood (such as skin biopsy) is warranted. While we do not accept this sample type directly, we can accept gDNA derived from skin or muscle, but deletion/duplication analysis is not guaranteed for gDNA samples because the success rate varies based on sample quality. Please see our Sample requirements page for more details.

For proposed recommendations to genetic counseling, testing, and clinical management, please refer to:
Churpek JE, et al. Proposal for the clinical detection and management of patients and their family members with familial myelodysplastic syndrome/acute leukemia predisposition syndromes. Leuk Lymphoma. 2013 Jan;54(1):28-35.

  1. Alter, BP, et al. Cancer in dyskeratosis congenita. Blood. 2009; 113(26):6549-57. PMID: 19282459
  2. Alter, BP, et al. Malignancies and survival patterns in the National Cancer Institute inherited bone marrow failure syndromes cohort study. Br. J. Haematol. 2010; 150(2):179-88. doi: 10.1111/j.1365-2141.2010.08212.x. PMID: 20507306
  3. Babushok, DV, Bessler, M. Genetic predisposition syndromes: when should they be considered in the work-up of MDS?. Best Pract Res Clin Haematol. 2015; 28(1):55-68. PMID: 25659730
  4. Bandipalliam, P. Syndrome of early onset colon cancers, hematologic malignancies & features of neurofibromatosis in HNPCC families with homozygous mismatch repair gene mutations. Fam. Cancer. 2005; 4(4):323-33. PMID: 16341812
  5. Churpek, JE, et al. Identifying familial myelodysplastic/acute leukemia predisposition syndromes through hematopoietic stem cell transplantation donors with thrombocytopenia. Blood. 2012; 120(26):5247-9. PMID: 23258901
  6. Churpek, JE, et al. Proposal for the clinical detection and management of patients and their family members with familial myelodysplastic syndrome/acute leukemia predisposition syndromes. Leuk. Lymphoma. 2013; 54(1):28-35. PMID: 22691122
  7. Dickinson, RE, et al. The evolution of cellular deficiency in GATA2 mutation. Blood. 2014; 123(6):863-74. PMID: 24345756
  8. Dokal, I. Dyskeratosis congenita. Hematology Am Soc Hematol Educ Program. 2011; 2011:480-6. PMID: 22160078
  9. German, J. Bloom's syndrome. XX. The first 100 cancers. Cancer Genet. Cytogenet. 1997; 93(1):100-6. PMID: 9062585
  10. Gonzalez, KD, et al. Beyond Li Fraumeni Syndrome: clinical characteristics of families with p53 germline mutations. J. Clin. Oncol. 2009; 27(8):1250-6. doi: 10.1200/JCO.2008.16.6959. PMID: 19204208
  11. Gumy, Pause, F, et al. ATM gene alterations in childhood acute lymphoblastic leukemias. Hum. Mutat. 2003; 21(5):554. PMID: 12673804
  12. Holme, H, et al. Marked genetic heterogeneity in familial myelodysplasia/acute myeloid leukaemia. Br. J. Haematol. 2012; 158(2):242-8. PMID: 22533337
  13. Klein, RD, Marcucci, G. Familial Acute Myeloid Leukemia (AML) with Mutated CEBPA. 2010 Oct 21. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 20963938
  14. Kratz, CP, et al. Cancer in Noonan, Costello, cardiofaciocutaneous and LEOPARD syndromes. Am J Med Genet C Semin Med Genet. 2011; 157C(2):83-9. PMID: 21500339
  15. Kratz, CP, et al. Cancer spectrum and frequency among children with Noonan, Costello, and cardio-facio-cutaneous syndromes. Br. J. Cancer. 2015; 112(8):1392-7. doi: 10.1038/bjc.2015.75. PMID: 25742478
  16. Krüger, L, et al. Cancer incidence in Nijmegen breakage syndrome is modulated by the amount of a variant NBS protein. Carcinogenesis. 2007; 28(1):107-11. PMID: 16840438
  17. Liew, E, Owen, C. Familial myelodysplastic syndromes: a review of the literature. Haematologica. 2011; 96(10):1536-42. PMID: 21606161
  18. Malkin, D, et al. Predisposition to pediatric and hematologic cancers: a moving target. Am Soc Clin Oncol Educ Book. 2014; :e44-55. PMID: 24857136
  19. Morrell, D, et al. Mortality and cancer incidence in 263 patients with ataxia-telangiectasia. J. Natl. Cancer Inst. 1986; 77(1):89-92. PMID: 3459930
  20. Nanri, T, et al. A family harboring a germ-line N-terminal C/EBPalpha mutation and development of acute myeloid leukemia with an additional somatic C-terminal C/EBPalpha mutation. Genes Chromosomes Cancer. 2010; 49(3):237-41. PMID: 19953636
  21. Owen, C, et al. Familial myelodysplasia and acute myeloid leukaemia--a review. Br. J. Haematol. 2008; 140(2):123-32. PMID: 18173751
  22. Owen, CJ, et al. Five new pedigrees with inherited RUNX1 mutations causing familial platelet disorder with propensity to myeloid malignancy. Blood. 2008; 112(12):4639-45. PMID: 18723428
  23. Pabst, T, et al. Somatic CEBPA mutations are a frequent second event in families with germline CEBPA mutations and familial acute myeloid leukemia. J. Clin. Oncol. 2008; 26(31):5088-93. PMID: 18768433
  24. Patil, S, Chamberlain, RS. Neoplasms associated with germline and somatic NF1 gene mutations. Oncologist. 2012; 17(1):101-16. PMID: 22240541
  25. Renneville, A, et al. Another pedigree with familial acute myeloid leukemia and germline CEBPA mutation. Leukemia. 2009; 23(4):804-6. PMID: 18946494
  26. Ruijs, MW, et al. TP53 germline mutation testing in 180 families suspected of Li-Fraumeni syndrome: mutation detection rate and relative frequency of cancers in different familial phenotypes. J. Med. Genet. 2010; 47(6):421-8. PMID: 20522432
  27. Schiffman, JD. Applying Molecular Epidemiology in Pediatric Leukemia. J. Investig. Med. 2015; :None. PMID: 25973690
  28. Sellick, GS, et al. Further evidence that germline CEBPA mutations cause dominant inheritance of acute myeloid leukaemia. Leukemia. 2005; 19(7):1276-8. PMID: 15902292
  29. Seminog, OO, Goldacre, MJ. Risk of benign tumours of nervous system, and of malignant neoplasms, in people with neurofibromatosis: population-based record-linkage study. Br. J. Cancer. 2013; 108(1):193-8. PMID: 23257896
  30. Smith, ML, et al. Mutation of CEBPA in familial acute myeloid leukemia. N. Engl. J. Med. 2004; 351(23):2403-7. PMID: 15575056
  31. Spinner, MA, et al. GATA2 deficiency: a protean disorder of hematopoiesis, lymphatics, and immunity. Blood. 2014; 123(6):809-21. PMID: 24227816
  32. Stieglitz, E, Loh, ML. Genetic predispositions to childhood leukemia. Ther Adv Hematol. 2013; 4(4):270-90. PMID: 23926459
  33. Takagi, M. [Genetics of hereditary hematological malignancies]. Rinsho Ketsueki. 2015; 56(10):1969-77. PMID: 26458435
  34. Tawana, K, et al. Disease evolution and outcomes in familial AML with germline CEBPA mutations. Blood. 2015; 126(10):1214-23. PMID: 26162409
  35. Varon, R, et al. Mutations in the Nijmegen Breakage Syndrome gene (NBS1) in childhood acute lymphoblastic leukemia (ALL). Cancer Res. 2001; 61(9):3570-2. PMID: 11325820
  36. Vasen, HF, et al. Guidelines for surveillance of individuals with constitutional mismatch repair-deficiency proposed by the European Consortium Care for CMMR-D" (C4CMMR-D). J. Med. Genet. 2014; 51(5):283-93. doi: 10.1136/jmedgenet-2013-102238. " PMID: 24556086
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  39. Wimmer, K, et al. Diagnostic criteria for constitutional mismatch repair deficiency syndrome: suggestions of the European consortium 'care for CMMRD' (C4CMMRD). J. Med. Genet. 2014; 51(6):355-65. doi: 10.1136/jmedgenet-2014-102284. PMID: 24737826
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Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Assay notes

If the patient has undergone a bone marrow transplant prior to genetic testing or currently has a hematological malignancy with actively circulating tumor cells, testing a sample type not derived from blood (such as skin biopsy) is warranted. While we do not accept this sample type directly, we can accept gDNA derived from skin or muscle, but deletion/duplication analysis is not guaranteed for gDNA samples because the success rate varies based on sample quality. Please see our Sample requirements page for more details.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
ATM NM_000051.3
BLM NM_000057.3
BRCA1 NM_007294.3
BRCA2 NM_000059.3
BRIP1 NM_032043.2
CEBPA NM_004364.4
CHEK2 NM_007194.3
CTC1 NM_025099.5
DKC1 NM_001363.4
EPCAM* NM_002354.2
ERCC4 NM_005236.2
FANCA NM_000135.2
FANCB NM_001018113.1
FANCC NM_000136.2
FANCD2* NM_033084.3
FANCE NM_021922.2
FANCF NM_022725.3
FANCG NM_004629.1
FANCI NM_001113378.1
FANCL NM_018062.3
FANCM NM_020937.2
GATA2 NM_032638.4
HRAS NM_005343.2
MLH1* NM_000249.3
MSH2* NM_000251.2
MSH6 NM_000179.2
NBN NM_002485.4
NF1 NM_000267.3
NHP2 NM_017838.3
NOP10 NM_018648.3
PALB2 NM_024675.3
PMS2 NM_000535.5
RAD51C NM_058216.2
RUNX1 NM_001754.4
SLX4 NM_032444.2
TERC NR_001566.1
TERT NM_198253.2
TINF2 NM_001099274.1
TP53* NM_000546.5
XRCC2 NM_005431.1

EPCAM: Analysis is limited to deletion/duplication analysis
FANCD2: Deletion/duplication analysis is not offered for exons 14-17.
MLH1: Deletion/duplication analysis covers the promoter region.
MSH2: Analysis includes the exon 1-7 inversion (Boland mutation).
TP53: Deletion/duplication analysis covers the promoter region.