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CLINICAL CAPABILITIES // Genetic testing

Hematologic Malignancy

Test for genetic indicators of blood-related cancers.

Clinical at Psomagen

Who Would Benefit from Hematologic Malignancy Genetic Testing?

1

A person with a strong family history of certain types of cancer

Determine if they carry a gene mutation that increases their risk. If they do have an inherited mutation, they might want to have screening tests to look for cancer early, or even take steps to try to lower their risk.

2

A person already diagnosed with cancer

This is especially true if there are other factors to suggest the cancer might have been caused by an inherited mutation (such as a strong family history or if the cancer was diagnosed at a young age). Genetic testing might show if the person has a higher risk of developing cancer. It can also help other family members decide if they want to be tested for the mutation.  

3

Family members of a person known to have an inherited gene mutation that increases their risk of cancer

Testing can help them know if they need screening tests to look for cancer early, or if they should take steps to try to lower their risk.

How Do I Order a Test?

A printed copy of the requisition form must be submitted with the specimen if you are not placing your order through the online portal. You can find and print a copy of the requisition form here. If you need to modify your order, please contact client services.

Hematologic Malignancy Panel Best Practices

Preferred Specimen

2mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)

Alternate Specimens

  • Saliva
  • Buccal swab
  • gDNA
Let's get started!

How to Ship Your Samples

Follow IATA Regulations

Please note that Psomagen sample collection kits are built to protect the samples from being damaged during transport and to comply with the International Air Transport Association (IATA) regulation. If you are using packaging other than that provided by Psomagen, please make sure to follow the "three layers of packaging" rule to avoid the risk of having the package destroyed by the courier:

  • A primary sample receptacle sealed (collection tube).
  • A leak-proof specimen bag containing absorbent material.
  • An outer packaging that meets the local postal regulations and is labeled as “Exempt Human Specimen.”

For more information please refer to page 187 of IATA Dangerous Goods Regulation.

Additional Shipment Requirements

For saliva, ship at room temperature (overnight shipping is not necessary).

For blood, we recommend using overnight shipping the same day that the blood is collected.

  • Blood can be kept at room temperature for up to 48 hours.
  • We request that blood is refrigerated no longer than two weeks.
  • Please do not freeze blood as deletion/duplication analysis is not supported for frozen or partially frozen blood.

Please ship the specimen in a crush-proof container via FedEx Priority Overnight (in accordance with the FedEx Packaging Guidelines for Clinical Samples.

Our US Shipping Address

Attn: Clinical Laboratory Testing Personnel
Psomagen Inc.
1330 Piccard Drive, Ste 103
Rockville, MD 20850

Test for 16 related genes

Gene List

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

Test Methodology and Limitations

DNA sequencing involves the extraction of genomic DNA from specimens collected in approved containers and provided the specimen meets required sample minimum quantity (e.g. volume, weight, etc). This is followed by quantification and qualification to ensure the adequacy of amount and purity for sequencing. Subsequently, whole exome sequencing is conducted on an IlluminaTM short read sequencing (SRS) platform (e.g., NovaSeq X PlusTM) at Psomagen, Inc.’s laboratories (CLIA # 21D2062464, CAP # 8742212).

DNA sequence alignment, variant calling, and variant filtering are performed utilizing the Illumina DRAGENTM bioinformatics pipeline (version 4.2.4.) and various tool sets, which align reads to the human reference genome (GRCh38) and identify single nucleotide variants (SNVs) and small insertions/deletions (InDels). Variant annotations are performed using a pipeline available in Fabric Enterprise. Variant review and interpretation are conducted according to the standards and guidelines set forth by the American College of Medical Genetics and Genomics (Richards S, et al., Genet Med., 2015) by Fabric Clinical Labs (CLIA #45D2281059, CAP # 9619501). Only variants classified as pathogenic or likely pathogenic are reported. The following quality filters are applied to all variants: coverage <40x, allele balance outside 0.3-0.7. Variants in the following genes are reported: ATM, BLM, CEBPA, EPCAM, GATA2, HRAS, MLH1, MSH2, MSH6, NBN, NF1, PMS2, RUNX1, TERC, TERT, TP53.

This test is designed to detect single nucleotide variants (SNVs) and small insertions/deletions (InDels). Next-Generation Sequencing (NGS) coverage may vary across the genome, potentially resulting in missed variants in regions with low coverage depth. Some genetic abnormalities may be undetectable with the current version of this test. While the DRAGEN bioinformatics pipeline demonstrates high accuracy for variant calling, there remains a possibility of false positive or false negative results due to variant interpretation which relies on current scientific knowledge and available databases. This may lead to the reclassification of reported variants as new information emerges from ongoing research and is updated in the ACMG guidelines. Furthermore, systematic chemical, computational, or human errors may contribute to false positives or false negatives of DNA variants. For any reported variants, confirmation by orthogonal technology and subsequent consultation with a genetic counselor or qualified healthcare provider can help to establish definitive risk. This result should be considered preliminary until such confirmation has been performed.

Clinical management for this individual should be based on personal and family history, along with other relevant information. If considered relevant to this individual’s clinical presentation and/or family history, targeted testing of appropriate family members of this individual for the reported variants may help to interpret these results. For assistance with the interpretation of these results, healthcare professionals may contact Psomagen directly at (301) 251-1007 or support@psomagen.com.

More Resources

  1. Furutani E, Shimamura A. Germline genetic predisposition to hematologic malignancy. J Clin Oncol. 2017;35(9):1018-1028. http://doi. org/10.1200/JCO.2016.70.8644

  2. Arber DA, Orazi A, Hasserjian R, et al. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute S. Ansar et al. 2377 leukemia. Blood. 2016;127(20):2391-2405. http://doi.org/10.1182/ blood-2016-03-643544

  3. University of Chicago Hematopoietic Malignancies Cancer Risk Team. How I diagnose and manage individuals at risk for inherited myeloid malignancies. Blood. 2016;128(14):1800-1813. http://doi.org/10.1182/ blood-2016-05-670240

  4. Desai AV, Perpich M, Godley LA. Clinical assessment and diagnosis of germline predisposition to hematopoietic malignancies: the University of Chicago experience. Front Pediatr. 2017;5:252. http://doi. org/10.3389/fped.2017.00252

  5. National Comprehensive Cancer Network, Myelodysplastic Syndromes V.3.2022, Updated January 13, 2022. Accessed May 2, 2022. https:// www.nccn.org/professionals/physician_gls/pdf/mds.pdf

  6. Baliakas P, Tesi B, Wartiovaara-Kautto U, et al. Nordic guidelines for germline predisposition to myeloid neoplasms in adults: recommendations for genetic diagnosis, clinical management and follow-up. Hemasphere. 2019;3(6):e321. http://doi.org/10.1097/HS9.0000000000 000321

  7. Trottier AM, Godley LA. Inherited predisposition to haematopoietic malignancies: overcoming barriers and exploring opportunities. Br J Haematol. 2021;194(4):663-676. http://doi.org/10.1111/bjh.17247

  8. Kohlmann W, Schiffman JD. Discussing and managing hematologic germ line variants. Hematology Am Soc Hematol Educ Program. 2016;2016(1):309-315. http://doi.org/10.1182/asheducation-2016.1.309

  9. 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. http://doi.org/10.1016/j.beha.2014.11. 004

  10. Kohne E. Hemoglobinopathies: clinical manifestations, diagnosis, and treatment. Dtsch Arztebl Int. 2011;108(31-32):532-540. http://doi.org/ 10.3238/arztebl.2011.0532

  11. Noris P, Pecci A. Hereditary thrombocytopenias: A growing list of disorders. Hematology Am Soc Hematol Educ Program. 2017; 2017(1):385-399. http://doi.org/10.1182/asheducation-2017.1.385

  12. Clifford M, Bannon S, Bednar EM, et al. Clinical applicability of proposed algorithm for identifying individuals at risk for hereditary hematologic malignancies. Leuk Lymphoma. 2019;60(12):3020-3027. http://doi.org/10.1080/10428194.2019.1630618

  13. Porter CC, Druley TE, Erez A, et al. Recommendations for surveillance for children with leukemia-predisposing conditions. Clin Cancer Res. 2017;23(11):e14-e22. http://doi.org/10.1158/1078-0432.CCR-17- 0428

  14. Imamura T. Genetic alterations of pediatric acute lymphoblastic leukemia. In: Kato M, ed. Genetic Alterations of Pediatric Acute Lymphoblastic Leukemia. Springer; 2020:9-19.

  15. Cerhan JR, Slager SL. Familial predisposition and genetic risk factors for lymphoma. Blood. 2015;126(20):2265-2273. http://doi.org/10. 1182/blood-2015-04-537498

  16. Herber M, Mertz P, Dieudonne Y, et al. Primary immunode ´ ficiencies and lymphoma: a systematic review of literature. Leuk Lymphoma. 2020;61(2):274-284. http://doi.org/10.1080/10428194.2019.1672 056

  17. Braunstein EM, Moliterno AR. Back to biology: new insights on inheritance in myeloproliferative disorders. Curr Hematol Malig Rep. 2014;9(4):311-318. http://doi.org/10.1007/s11899-014-0232-3

  18. Rumi E, Passamonti F, Della Porta MG, et al. Familial chronic myeloproliferative disorders: clinical phenotype and evidence of disease anticipation. J Clin Oncol. 2007;25(35):5630-5635. http://doi.org/ 10.1200/JCO.2007.12.6896

  19. Bellanne-Chantelot C, Rabadan Moraes G, Schmaltz-Panneau B, ´ Marty C, Vainchenker W, Plo I. Germline genetic factors in the pathogenesis of myeloproliferative neoplasms. Blood Rev. 2020;42: 100710. http://doi.org/10.1016/j.blre.2020.100710

  20. Hahn CN, Wee A, Babic M, et al. Duplication on chromosome 14q identified in familial predisposition to myeloid malignancies and myeloproliferative neoplasms. Blood. 2017;130(Suppl 1):492. http:// doi.org/10.1182/blood.V130.Suppl_1.492.492

Our Certifications

CLIA ID number: 21D2062464
CAP ID number: 8742212