Genetic studies by NGS Panels

Panel for bone marrow failure (Code 10111)

NGS-10111-v15
BRCA1 BRCA2 BRIP1 ERCC4
FANCA FANCB FANCC FANCD2
FANCE FANCF FANCG FANCI
FANCL FANCM MAD2L2 PALB2
RAD50 RAD51C RFWD3 SLX4
UBE2T XRCC2 RPS19 RPS24
RPL5 RPL11 RPS7 RPS10
RPS26 RPL26 RPL15 RPS29
TSR2 GATA1 RPL19 RPS28
RPL27 RPL31 RPS27 RPS15
RPS27A RPL36 RPL9 RPS17
TERC TERT NHP2/NOLA TINF2
NOP10/NOLA3 WRAP53 RTEL1 DKC1
USB1 CTC1 PARN ACD
RPL35A

 

This panel combines the panels with code 10090 + 10100 + 10110.

Fanconi anemia (FA) (OMIM #227645, #227645, #227646, #227650, #300514, #600901, #603467, #609053, #609054, #610832,  #613390,  #613951,  #614082,  #614083,  #615272, #616435, #617243, #617244, #617247) is a complex inherited disorder where genes involved in DNA repair and genomic stability are affected. 22 genes associated with the disease have been identified.

The pattern of inheritance is usually autosomal recessive but there have been described cases with an X-linked transmission (FANCB gene) and cases of autosomal dominant inheritance (FANCR gene). Mutations of the FANCA gene are the most represented (70-80% in our environment).

The initial diagnostic test should be the evaluation of chromosomal fragility in lymphocytes induced by diepoxybutane (DEB) or mitomycin (MMC). In uncertain or negative cases with high clinical suspicion, the study in fibroblasts should be performed due to the phenomenon of somatic mosaicism. To complete the diagnosis of FA it is essential the characterization of the subtype and pathogenic mutations of the disease, since it confirms the diagnosis and enables the detection of carriers, as well as facilitates prenatal and pre-implantation diagnosis.

The estimated heterozygous carrier frequency is 0.3-1%, with an expected prevalence of at least 1-9 / 1,000,000 births. In some populations, the frequency of carriers is much higher, due to founder mutations, although it is distributed by all races and ethnic groups. To date, more than 2,000 cases have been described.

 

Regarding clinical manifestations, bone marrow failure usually appears around 7 years of age. In the course of the disease, 90-98% of patients will develop marrow failure before age 40. This characteristic, as well as the higher incidence of tumors, seem related to many other factors and not only to DNA damage: an excess of free oxygen radicals has been described in Fanconi cells, as well as some mitochondrial defects. Patients may develop acute myeloid leukemia, often preceded by myelodysplastic syndrome; They are also very predisposed to develop solid tumors in the head, neck or anogenital region. In 2/3 of patients, the first signs of AF are congenital malformations that can affect the skeleton, the skin, and the urogenital, cardiopulmonary, gastrointestinal, and central nervous systems. Minor abnormalities such as low weight and height, microcephaly, and / or microphthalmia may also occur. Abnormalities in the pigmentation and hypoplasia of thenar eminence are frequent. Almost 20% of patients have ear malformations. Congenital malformations can vary in the same family. When congenital malformations are not prominent, the diagnosis may be delayed until the onset of bone marrow failure. Fertility is very damaged in men, and very affected in half of women. Pregnancy is often complicated.

 

AF should be considered in all cases of young patients with bone marrow failure of unknown origin. In the differential diagnosis, other syndromes predisposing to cancer or with pancytopenia should be considered (Diamond-Blackfan anemia, immune pancytopenia).

Supportive treatment includes transfusions of packed red cells or platelets. The only curative treatment for haematological manifestations is the transplantation of hematopoietic progenitor cells (HSCT). In HSCT from family donors, the use of reduced intensity conditioning with fludarabine and depletion of T lymphocytes in the inoculum is giving excellent results, with improved survival and decreased incidence of secondary neoplasms. Unfortunately, in most cases there is no family donor so it is necessary to resort to unrelated donors or the umbilical cord. Survival is around 70%. However, this process tends to increase the risk of solid tumor, which must be followed with special attention. Gene therapy is in very advanced stages of research. Symptomatic treatment includes the administration of oral androgens, which improves blood parameters, especially the number of red blood cells. The administration of hematopoietic growth factors should be considered if necessary. As malignant tumors develop, the treatment becomes more complicated due to the patient’s radiation sensitivity and chemotherapy.

Bone marrow insufficiency and malignant tumors lead to an unfavorable prognosis with a reduced life expectancy, which has improved thanks to HSCT and androgen treatment.

 

DiamondBlackfan anaemia (DBA) is a rare congenital erythroblastopenia and inherited bone marrow failure syndrome that is clinically and genetically very heterogeneous (Vlachos et al., 2008). It is characterized by pure red cell aplasia and physical malformations in about 50% of all DBA patients. It affects approximately seven individuals in every million live births.

 

Clinical presentation is detected normally during the first year of life in classical DBA forms, but late-onset DBA forms in adolescents or adults have also been described.

 

Clinical signs and symptoms of the classic form of DBA comprise a profound normochromic and usually macrocytic anaemia with normal leukocytes and platelets, growth retardation in 30% of affected individuals and congenital malformations (in up to 50% of affected individuals) including craniofacial and thumb deformities, short stature, cardiac and urogenital malformations. In the classical form, the hematologic complications occur in 90% of affected individuals during the first year of life. Basic hallmarks of anaemia include pale pallor, failure to thrive, and feeding difficulties. Neurological or cognitive problems are very rare in DBA. DBA patients generally exhibit high erythropoietin levels, increased levels of foetal haemoglobin (unspecific markers that are also elevated in other bone marrow diseases) and, as DBA-specific marker, elevated activity of the erythrocyte adenosine deaminase enzyme (eADA), prior to transfusion, is presented in 80-85% of all patients (Fargo et al. 2013). The risk of DBA patients developing cancer is higher than normal (Vlachos et al. 2012). DBA is associated with an increased risk for acute myelogenous leukaemia (AML), myelodysplastic syndrome (MDS), and solid tumours including osteogenic sarcoma.

 

The phenotypic spectrum ranges from a mild form (e.g., mild anaemia, no anaemia with only subtle erythroid abnormalities, physical malformations without anaemia) to a severe form of foetal anaemia resulting in non-immune hydrops fetalis.

 

The diagnosis of classical DBA form is established in a proband when all four of the following diagnostic criteria are present:

  • Age younger than one year
  • Macrocytic anaemia with no other significant cytopenias
  • Reticulocytopenia
  • Normal marrow cellularity with a paucity of erythroid precursors

Differential diagnoses include parvovirus B19-associated pure red cell aplasia and transient erythroblastipenia, these latest patients show normal MCV, eADA and HbF values. In late-onset DBA or delayed diagnostic cases (adolescents or adults) bone marrow might display hypocellularity with dysplasias and megaloblastic changes resembling low grade MDS or 5q- syndrome. Other causes of bone marrow failure (e.g., Fanconi anaemia, Pearson syndrome, dyskeratosis congenital, human immunodeficiency virus infection) should be ruled out as appropriate.

 

Genetic causes of DBA and Genetic counselling

DBA is considered a ribosomopathy, as this disorder is almost exclusively driven by haploinsufficient mutations in a ribosomal protein (RP) gene and results in a pre-ribosomal RNA (rRNA) maturation defect (Dianzani and Loreni, 2008). In about 30% of diagnosed patients no mutation is found (Wegman-Ostrosky and Savage 2017).

 

DBA has been associated with pathogenic variants in several genes that encode ribosomal proteins (RP genes) and in GATA1 and TSR2 genes (see table above).

 

DBA due to mutation in RP genes is inherited in an autosomal dominant manner, as based on animal model homozygous mutations are suspected to be lethal. GATA1-related and TSR2-related DBA are inherited in an X-linked manner.

Approximately 40% to 45% of individuals with autosomal dominant DBA have inherited the pathogenic variant from a parent; approximately 55% to 60% have a sporadic or de novo pathogenic variant. In several familial cases with a proband inheriting the mutation from a parent, the parent will not show any overt phenotype and is considered a “silent carrier”. Silent carriers may also exhibit only a macrocytosis without anaemia and or an elevated eADA.

 

Each child of an individual with autosomal dominant DBA has a 50% chance of inheriting the pathogenic variant. Males with GATA1 orTSR2-related DBA pass the pathogenic variant to all of their daughters and none of their sons. Women heterozygous for a GATA1 or TSR2 pathogenic variant have a 50% chance of transmitting the pathogenic variant in each pregnancy: males who inherit the pathogenic variant will be affected; females who inherit the pathogenic variant will be carriers and will usually not be affected.

 

Carrier testing of at-risk female relatives is possible if the GATA1 or TSR2 pathogenic variant has been identified in the family. Prenatal testing for pregnancies at increased risk is possible if the familial pathogenic variant has been identified.

 

Management (Shimamura and Alter, 2010; , Vlachos and Muir, 2010, Horos and von Lindern, 2012)

Treatment of manifestations: Corticosteroid treatment, recommended in children older than age twelve months, initially improves the red blood cell count in approximately 80% of affected individuals. Chronic transfusion with packed red blood cells is initially necessary while the diagnosis is made and in those not responsive to corticosteroids. Hematopoietic stem cell transplantation (HSCT), the only curative therapy for the hematologic manifestations of DBA, is often recommended for those who are transfusion dependent or develop other cytopenias. Treatment of malignancies should be coordinated by an oncologist. Chemotherapy must be given cautiously as it may lead to prolonged cytopenia and subsequent toxicities.

Prevention of secondary complications: Transfusion-related iron overload is the most common complication in transfusion-dependent individuals. Iron chelation therapy with deferasirox orally or desferrioxamine subcutaneously is recommended after ten to 12 transfusions. Corticosteroid-related side effects must also be closely monitored, especially as related to risk for infection, growth retardation, and loss of bone density in growing children. Often individuals will be placed on transfusion therapy if these side effects are intolerable.

Surveillance: Complete blood counts several times a year; bone marrow aspirate/biopsy periodically to evaluate morphology and cellularity in the event of another cytopenia or a change in response to treatment. In steroid-dependent individuals: monitor blood pressure and (in children) growth.

Agents/circumstances to avoid: Deferiprone for the treatment of iron overload, which has led to severe neutropenia in a few individuals with DBA; infection (especially those on corticosteroids).

Evaluation of relatives at risk: Molecular genetic testing of at-risk relatives of a proband with a known pathogenic variant allows for early diagnosis and appropriate monitoring for bone marrow failure, physical abnormalities, and related cancers.

 

Dyskeratosis congenital (DC) (OMIM #127550, #224230, #305000, #613987, #613988, #613989, #613990, #615190, #616353) is a multisystem disease with a very low incidence (<1 / 1,000,000 newborns), with defects in the maintenance of chromosomal telomeres. It is characterized mainly by mucocutaneous alterations, of which the classic triad stands out: oral leukoplakia, nail dystrophy and alteration of skin pigmentation (Zinnser, 1906). These manifestations do not necessarily occur in all individuals, neither at diagnosis nor throughout the disease. The symptoms can be very variable, both for the time of appearance of these in a same individual and for manifestations in members of the same family. Other organs mainly affected are the bone marrow (80% of marrow failure before the age of 30), the lung and the liver, in which its parenchyma is replaced by fat or fibrosis, affecting its function. Other manifestations may be: growth disorders, head and neck alterations (microcephaly, strabismus, cataracts, …), esophageal stenosis, anal mucosal leukoplakia, genitourinary alterations, osteoporosis, mental retardation, ataxia, immunodeficiency, or neoplasms (squamous carcinoma, pancreatic carcinoma, acute myeloblastic leukemia or Hodgkin’s lymphoma).

 

Telomeres are exanucleotides (TTAGGG) that shorten in each cell division; there is a telomerase complex that acts as protector of the telomeres, favoring its extension although incompletely, and a regulatory complex, protective of telomerase activity, called shelterin. An excessive shortening of telomeres involves apoptosis or cell death, so that the cells lose the ability to replicate earlier than expected for their age.

 

Patients with DC have mutations in genes that code for the telomerase complex and for the protective complex or shelterin.

The most frequent presentation of the disease is that produced by mutations in the DKC1 gene, which codes for the dyskerin protein and is X-linked inheritance. However, mutations have recently been described in other genes involved (POT1, TERC, TERD, PARN …)

 

The differential diagnosis should be made along with other syndromes of congenital marrow failure (Fanconi anemia, Blackfan-Diamond anemia and Swachman-Diamond syndrome), acquired medullary aplasia and idiopathic pulmonary fibrosis in young patients.

 

The treatment must target the affected organs; marrow failure is one of the most frequent and early complications, whose only curative treatment is hematopoietic progenitor stem cell transplantation (HSCT) with reduced intensity conditioning (myeloablative conditioning is contraindicated due to the high toxicity related to the procedure). HSCT should be performed without delay in patients with severe pancytopenia and compatible donor. Otherwise, response to androgenic derivatives (50-70% of cases) such as oxymetholone and danazol has been demonstrated. In those patients without other alternatives, transfusional support should be performed.

The main causes of death are related to bone marrow failure, cancer and lung disease, particularly fibrosis. Cancer usually develops after the third decade. The most common solid malignancies are squamous cell carcinoma of the head and neck.

References

  • Ghemlas I, Li H, Zlateska B, Klaassen R, Fernandez CV, Yanofsky RA et al. Improving diagnostic precision, care and syndrome definitions using comprehensive next-generation sequencing for the inherited bone marrow failure syndromes. J Med Genet. 2015;52:575-84.
  • Dietz AC, Mehta PA, Vlachos A, Savage SA, Bresters D, Tolar J et al. Current Knowledge and Priorities for Future Research in Late Effects after Hematopoietic Cell Transplantation for Inherited Bone Marrow Failure Syndromes: Consensus Statement from the Second Pediatric Blood and Marrow Transplant Consortium International Conference on Late Effects after Pediatric Hematopoietic Cell Transplantation. Biol Blood Marrow Transplant. 2017;23:726-735.
  • MacMillan ML1, Wagner JE. Haematopoeitic cell transplantation for Fanconi anaemia – when and how? Br J Haematol. 2010;149:14-21
  • Alter BP. Fanconi anemia and the development of leukemia. Best Pract Res Clin Haematol. 2014;27:214-21
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  • Dianzani, I., Loreni, F., 2008. Diamond-Blackfan anemia: a ribosomal puzzle. Haematologica 93 (11), 1601-1604.
  • Fargo, J.H., Kratz, C.P., Giri, N., Savage, A., Wong, C., Backer, K., et al., 2013. Erythrocyte adenosine deaminase: diagnostic value for Diamond-Blackfan anaemia. Br. J. Haematol. 160 (4), 547-554 PubMed PMID: 23252420.
  • Horos, R., von Lindern, M., 2012. Molecular mechanisms of pathology and treatment in diamond blackfan anaemia. J. Haematol. 159 (5), 514-527
  • Shimamura, A., Alter, B.P., 2010. Pathophysiology and management of inherited bone marrow failure syndromes. Blood Rev. 24 (3), 101-122.
  • Vlachos, A., Ball, S., Dahl, N., Alter, B.P., Sheth, S., Ramenghi, U., et al., 2008. Diagnosing and treating Diamond Blackfan anaemia: results of an international clinical consensus conference. J. Haematol. 142 (6), 859-876.
  • Vlachos, A., Muir, E., 2010. How I treat Diamond-Blackfan anemia. Blood 116 (19), 3715-3723
  • Vlachos, A., Rosenberg, P.S., Atsidaftos, E., Alter, B.P., Lipton, J.M., 2012. Incidence of neoplasia in diamond blackfan anemia: a report from the diamond blackfan anemia registry. Blood 119 (16), 3815-3819.
  • Wegman-Ostrosky, T., Savage, S.A., 2017. The genomics of inherited bone marrow failure: from mechanism to the clinic. J. Haematol. 177 (4), 526-542
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