Using MS-MLPA as an efficient screening tool for detecting 9p21 abnormalities in pediatric acute lymphoblastic leukemia.

BACKGROUND: Characterization of recurrent genetic lesions in childhood acute lymphoblastic leukemia (ALL) has enabled therapeutic stratification with improved outcomes. The tumor suppressor genes, CDKN2A and CDKN2B, encoding p16(INK4a) , p14(ARF) , and p15(INK4b) have been localized to 9p21. Abnormalities of 9p21 have been reported in 10-30% of childhood ALL using conventional cytogenetics and fluorescence in situ hybridization (FISH). The incidence of 9p21 using more sensitive techniques, such as methylation specific multiplex ligation-dependent probe amplification (MS-MLPA), remains uncertain, and thus also the prognostic significance. PROCEDURE: We investigated the incidence and prognostic importance of 9p21 abnormalities in pediatric ALL patients using MS-MLPA and compared these results to FISH. RESULTS: In total, MS-MLPA or FISH detected aberrations (both dosage and methylation abnormalities) at 9p21 in a remarkable 32/48 (67%) patients in contrast to a much lower rate of only 8% of patients identified to have deletions by standard G banding cytogenetics. MS-MLPA identified five deletions not found by FISH. Aberrant methylation at CDKN2B was found in 19 (46%) patients. 9p21 abnormalities were associated with National Cancer Institute (NCI) high-risk criteria (P = 0.04) and were present in all five patients with T-cell disease. Four pre-B-cell ALL patients relapsed, three of whom had prior 9p21 abnormalities. CONCLUSIONS: MS-MLPA had a higher detection rate for 9p21 abnormalities than previously reported for other techniques. Given the ease of processing, minimal equipment and low cost of MS-MLPA, our results suggest that previous reports may have underestimated the true frequency of 9p21 abnormalities and their potential impact upon ALL outcome.

Is gene discovery research or diagnosis?

The criteria that distinguish human genetic research from clinical molecular diagnosis are frequently practical rather than theoretical. They are driven by the availability and costs of the relevant technologies and the systemic level of scientific fluency in interpreting laboratory results. The guiding principle in the practice of medicine is the primacy of patient care. In the service of this overarching goal the defining characteristic of clinical diagnosis is the definition of the disease entity, even when no immediate treatment is possible. For heritable disorders caused by single-gene defects, identifying the putative causal variant is the goal of molecular diagnostics. Current technologies, costs, and standards of institutional infrastructure have not typically permitted novel gene discovery to be performed within the realm of the clinical laboratory. Discovery is usually funded by self-defined research organizations and carried out by self-defined research personnel with the primary intent of publishing findings in research journals. However, exponential improvements in technological capabilities and the concurrent decline in associated costs seem poised to recast this landscape, bringing to clinical medicine some activities now considered research. Even whole genome resequencing of individual patient DNA is within clinical reach in the foreseeable future.

JAK2 V617F positive polycythemia Vera in a child with neurofibromatosis type I.

We report a child with polycythemia vera (PV). This patient demonstrates the acquired somatic JAK2 V617F mutation and also has neurofibromatosis type I (NF1). NF1, while not previously associated with PV, is associated with another childhood MPD, juvenile myelomonocytic leukemia (JMML). Thus we examined a number of genetic abnormalities identified in JMML patients, but found no association in this case. Neurofibromin sequencing failed to identify a causative mutation. An unknown genetic abnormality resulting in NF1 may have predisposed this young child to acquiring the common JAK2 mutation.

Congenital isolated adrenocorticotropin deficiency: an underestimated cause of neonatal death, explained by TPIT gene mutations.

Tpit is a T box transcription factor important for terminal differentiation of pituitary proopiomelanocortin-expressing cells. We demonstrated that human and mouse mutations of the TPIT gene cause a neonatal-onset form of congenital isolated ACTH deficiency (IAD). In the absence of glucocorticoid replacement, IAD can lead to neonatal death by acute adrenal insufficiency. This clinical entity was not previously well characterized because of the small number of published cases. Since identification of the first TPIT mutations, we have enlarged our series of neonatal IAD patients to 27 patients from 21 unrelated families. We found TPIT mutations in 17 of 27 patients. We identified 10 different TPIT mutations, with one mutation found in five unrelated families. All patients appeared to be homozygous or compound heterozygous for TPIT mutations, and their unaffected parents are heterozygous carriers, confirming a recessive mode of transmission. We compared the clinical and biological phenotype of the 17 IAD patients carrying a TPIT mutation with the 10 IAD patients with normal TPIT-coding sequences. This series of neonatal IAD patients revealed a highly homogeneous clinical presentation, suggesting that this disease may be an underestimated cause of neonatal death. Identification of TPIT gene mutations as the principal molecular cause of neonatal IAD permits prenatal diagnosis for families at risk for the purpose of early glucocorticoid replacement therapy.

VHL P25L is not a pathogenic von Hippel-Lindau mutation: a family study.

BACKGROUND: von Hippel-Lindau (VHL) disease is a hereditary tumor syndrome in which affected individuals may develop CNS and retinal hemangioblastomas, pheochromocytomas, renal cell carcinoma, and cysts of various organs. The VHL gene has been localized to chromosome 3p25-26 and >500 germline mutations have been identified. A rare variant of the VHL gene results in the substitution of lysine for proline at position 25 (P25L) in the larger of the two VHL proteins. This VHL variant has previously been described in a limited number of cases and has been strongly suggested to be non-pathogenic, but this has not been proven. METHODS: A family with a medical history suggestive of VHL disease was investigated using DNA sequence analysis to determine the presence of the P25L variant of the VHL protein. RESULTS: Sequence analysis identified the VHL P25L variant in 7 of 14 family members, one of whom had a single retinal hemangioma, which is in itself insufficient to diagnose VHL disease. The variant was not identified in a family member with clear cell renal carcinoma, which is a hallmark feature of VHL disease. CONCLUSIONS: On the basis of these results, it is concluded that P25L is a benign variant of the VHL protein and individuals carrying this variant should not be required to undergo screening for VHL manifestations.