Hereditary Bone Marrow Failure Panel, Sequencing and Deletion/Duplication

Content Review: August 2022 Last Update:
  • Use to assess for inherited/germline DNA variants associated with bone marrow failure or hereditary predisposition to myeloid neoplasms.
  • Preferred sample type is cultured skin fibroblasts; testing whole blood in affected patients may not definitively determine germline status.
  • Not intended to detect somatic variants; refer to the Laboratory Test Directory for myeloid malignancy panel testing.

Bone marrow failure (BMF) encompasses a heterogenous array of acquired and germline conditions characterized by qualitative or quantitative defects in one or more hematopoietic lineages resulting in cytopenias and hypocellular bone marrow. These include inherited syndromes such as Fanconi anemia (FA), telomere biology disorders (TBD) such as dyskeratosis congenita (DC), Schwachman-Diamond syndrome (SDS), Diamond-Blackfan anemia (DBA), congenital amegakaryocytic thrombocytopenia (CAMT), severe congenital neutropenia (SCN), aplastic anemia, and others.

This panel includes genes causative for hereditary BMF syndromes as well genes associated with hereditary predisposition to myeloid neoplasms, as there is often clinical overlap between these two entities.

Disease Overview

Hereditary BMF syndromes are caused by germline pathogenic variants that disrupt DNA repair, telomere maintenance, ribosome biogenesis, and structural protein pathways. In addition to BMF, these conditions may also be accompanied by syndromic physical findings and predisposition to hematologic and other malignancies. While most patients with hereditary BMF present in childhood, these conditions may manifest at any age.

Genetics

Genes

For a list of genes tested, associated disorders, and inheritance, refer to the Genes Tested table.

Refer to Limitations for exons not covered by sequencing and genes for which deletion and/or duplication is not available.

Test Interpretation

Methodology

This test is performed using the following sequence of steps:

  • Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
  • Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing, or NGS) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for the detection of large deletions and duplications.
  • Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
  • Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.

Analytic Sensitivity/Specificity

Variant Class Analytic Sensitivity (PPA) Estimatea (%) and 95% Credibility Region Analytic Specificity (NPA) Estimate (%)

SNVs

>99 (96.9-99.4)

>99.9

Deletions 1-10 bpb

93.8 (84.3-98.2)

>99.9

Insertions 1-10 bpb

94.8 (86.8-98.5)

>99.9

Exon-levelc deletions

97.8 (90.3-99.8) [2 exons or larger]

62.5 (38.3-82.6) [single exon]

>99.9

Exon-levelc duplications

83.3 (56.4-96.4) [3 exons or larger]

>99.9

aPPA values are derived from larger methods-based MPS and/or Sanger validations. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA) unless otherwise indicated.

bVariants greater than 10 bp may be detected, but the analytic sensitivity may be reduced.

cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp.

bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants

Limitations

  • A negative result does not exclude a diagnosis of bone marrow failure.
  • Diagnostic errors can occur due to rare sequence variations.
  • Interpretation of this test result may be impacted if this patient received an allogeneic stem cell transplant unless the sample analyzed is definitively from the recipient, such as cultured skin fibroblasts.
  • The germline or somatic status of a detected variant cannot be definitively determined in patients with hematologic malignancy if the assay is performed on blood or other tissue that may be contaminated by clonal or malignant cells; testing a definitively germline specimen such as cultured fibroblasts may be recommended in such cases.
  • The following will not be evaluated:
    • Variants outside the coding regions and intron-exon boundaries of targeted genes
    • SBDS gene associated with Schwachman-Diamond syndrome
    • Regulatory region and deep intronic variants
    • SNVs and small insertions/deletions will not be called in the following exons due to technical limitations of the assay:
      • CXCR4 (NM_001348056) exon 2
      • CXCR4 (NM_001348059) exon 2
      • DNAJC21 (NM_001348420) partial exon 9 (Chr5:34945827-34945845)
      • ERCC6L2 (NM_001375291) exon 19
      • ERCC6L2 (NM_001375292) exon 19
      • ERCC6L2 (NM_001375293) exon 18
      • ERCC6L2 (NM_001375294) exon 18
      • FANCA (NM_001018112) exon 11
      • FANCA (NM_001351830) exon 10
      • FANCD2 (NM_033084) exons 14, 17, 21, 22
      • FANCD2 (NM_001018115) exons 14, 17, 21, 22
      • FANCD2 (NM_001319984) exons 14, 17, 21, 22
      • FANCD2 (NM_001374253) exons 14, 17, 20, 21
      • FANCD2 (NM_001374254) exons 14, 17, 21, 22
      • FANCD2 (NM_001374255) exon 10
      • FANCL (NM_001374615) exon 8
    • Deletions/duplications in CEBPA, NOP10, RMRP, and RPL15 genes
    • Duplications in the TERC gene
    • Breakpoints of large deletions/duplications
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by massively parallel sequencing
    • Large duplications less than 3 exons in size
    • Noncoding transcripts
    • Some variants due to technical limitations in the presence of pseudogenes and/or repetitive/homologous regions
    • Low-level somatic variants

Genes Tested

Gene MIM # Disorders Inheritance

ACD

609377

Dyskeratosis congenita

AD, AR

ALAS2

301300

Sideroblastic anemia

Erythropoietic protoporphyria

XL

ANKRD26

610855

Thrombocytopenia 2

AD

ATM

607585

Ataxia-telangiectasia

AR

BLM

604610

Bloom syndrome

AR

BRCA1

113705

Fanconi anemia, complementation group S

AR

Hereditary breast and ovarian cancer syndrome AD

BRCA2

600185

Fanconi anemia, complementation group D1

AR

Hereditary breast and ovarian cancer syndrome AD

BRIP1

605882

Fanconi anemia, complementation group J

AD

CBL

165360

Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia

AD

CEBPA

116897

Familial acute myeloid leukemia

AD

CSF3R

138971

Severe congenital neutropenia 7

AR

CTC1

613129

Dyskeratosis congenita

Coats plus syndrome

AR

CXCR4

162643

WHIM syndrome

AD

DDX41

608170

Familial myeloproliferative/lymphoproliferative neoplasms

AD

DKC1

300126

Dyskeratosis congenita

XL

DNAJC21

617048

Bone marrow failure syndrome 3

AR

ELANE

130130

Cyclic neutropenia

Severe congenital neutropenia 1

AD

ERCC4

133520

Xeroderma pigmentosum, group F

Fanconi anemia, complementation group Q

AR

ERCC6L2

615667

Bone marrow failure syndrome 2

AR

ETV6

600618

Thrombocytopenia 5

AD

FANCA

607139

Fanconi anemia, complementation group A

AR

FANCB

300515

Fanconi anemia, complementation group B

XL

FANCC

613899

Fanconi anemia, complementation group C

AR

FANCD2

613984

Fanconi anemia, complementation group D2

AR

FANCE

613976

Fanconi anemia, complementation group E

AR

FANCF

613897

Fanconi anemia, complementation group F

AR

FANCG

602956

Fanconi anemia, complementation group G

AR

FANCI

611360

Fanconi anemia, complementation group I

AR

FANCL

608111

Fanconi anemia, complementation group L

AR

G6PC3

611045

Dursun syndrome

Severe congenital neutropenia 4

AR

GATA1

305371

Dyserythropoietic anemia and thrombocytopenia

XL

GATA2

137295

Familial acute myeloid leukemia and myelodysplastic syndrome

AD

GFI1

600871

Severe congenital neutropenia 2

AD

HAX1

605998

Severe congenital neutropenia 3

AR

HOXA11

142958

Radioulnar synostosis with amegakaryocytic thrombocytopenia 1

AD

IKZF1

603023

Common variable immunodeficiency 13

AD

KRAS

190070

Noonan syndrome

AD

MBD4

603574

Susceptibility to acute myeloid leukemia

Unknown

MPL

159530

Congenital amegakaryocytic thrombocytopenia (CAMT)

AR

MYH9

160775

Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

AD

NBN

602667

Aplastic anemia

Nijmegen breakage syndrome

AR

NHP2

606470

Dyskeratosis congenita

AR

NOP10

606471

Dyskeratosis congenita

AR

NRAS

164790

Noonan syndrome

AD

PALB2

610355

Fanconi anemia, complementation group N

AR

PARN

604212

Dyskeratosis congenita

AR

Pulmonary fibrosis and/or bone marrow failure AD

PTPN11

176876

Noonan syndrome

AD

RAD51C

602774

Fanconi anemia, complementation group O

AR

RMRP

157660

Aplastic anemia

Cartilage-hair hypoplasia

AR

RPL11

604175

Diamond-Blackfan anemia 7

AD

RPL15

604174

Diamond-Blackfan anemia 12

AD

RPL26

603704

Diamond-Blackfan anemia 11

AD

RPL35A

180468

Diamond-Blackfan anemia 5

AD

RPL5

603634

Diamond-Blackfan anemia 6

AD

RPS10

603632

Diamond-Blackfan anemia 9

AD

RPS19

603474

Diamond-Blackfan anemia 1

AD

RPS24

602412

Diamond-Blackfan anemia 3

AD

RPS26

603701

Diamond-Blackfan anemia 10

AD

RPS7

603658

Diamond-Blackfan anemia 8

AD

RTEL1

608833

Pulmonary fibrosis and/or bone marrow failure

AD

Dyskeratosis congenita AD, AR

RUNX1

151385

Familial platelet disorder with associated myeloid malignancy

AD

SAMD9

610456

Monosomy 7 myelodysplasia and leukemia syndrome

MIRAGE syndrome

AD

SAMD9L

611170

Monosomy 7 myelodysplasia and leukemia syndrome

Ataxia-pancytopenia syndrome

AD

SLX4

613278

Fanconi anemia, complementation group P

AR

SRP72

602122

Bone marrow failure syndrome 1

AD

TERC

602322

Dyskeratosis congenita

Pulmonary fibrosis

AD

TERT

187270

Dyskeratosis congenita

AD, AR

TET2

612839

Immunodeficiency

AR

TINF2

604319

Dyskeratosis congenita

AD

TP53

191170

Li-Fraumeni syndrome

Bone marrow failure syndrome 5

AD

UBE2T

610538

Fanconi anemia, complementation group T

AR

USB1

613276

Poikiloderma with neutropenia

AR

VPS45

610035

Severe congenital neutropenia

AR

WAS

300392

Wiskott-Aldrich syndrome,

Severe congenital neutropenia

Thrombocytopenia

XL

WRAP53

612661

Dyskeratosis congenita

AR