Deep Sequencing of Cell-Free Peripheral Blood DNA as a Reliable Method for Confirming the Diagnosis of Myelodysplastic Syndrome.

BACKGROUND: Demonstrating the presence of myelodysplastic syndrome (MDS)-specific molecular abnormalities can aid in diagnosis and patient management. We explored the potential of using peripheral blood (PB) cell-free DNA (cf-DNA) and next-generation sequencing (NGS). MATERIALS AND METHODS: We performed NGS on a panel of 14 target genes using total nucleic acid extracted from the plasma of 16 patients, all of whom had confirmed diagnoses for early MDS with blasts <5%. PB cellular DNA from the same patients was sequenced using conventional Sanger sequencing and NGS. RESULTS: Deep sequencing of the cf-DNA identified one or more mutated gene(s), confirming the diagnosis of MDS in all cases. Five samples (31%) showed abnormalities in cf-DNA by NGS that were not detected by Sanger sequencing on cellular PB DNA. NGS of PB cell DNA showed the same findings as those of cf-DNA in four of five patients, but failed to show a mutation in the RUNX1 gene that was detected in one patient's cf-DNA. Mutant allele frequency was significantly higher in cf-DNA compared with cellular DNA (p = 0.008). CONCLUSION: These data suggest that cf-DNA when analyzed using NGS is a reliable approach for detecting molecular abnormalities in MDS and should be used to determine if bone marrow aspiration and biopsy are necessary.

Supernumerary marker chromosomes detected in 100,000 prenatal diagnoses: molecular cytogenetic studies and clinical significance.

OBJECTIVE: To evaluate the clinical significance of the supernumerary marker chromosomes (SMCs) detected during prenatal diagnosis. METHODS: We retrospectively studied cytogenetic/fluorescence in situ hybridization (FISH) results and clinical evaluation of 110 marker cases identified from approximately 100,000 cases referred for prenatal diagnosis. The clinical follow-up performed was focused on cases with de novo markers not derived from chromosome 15. RESULTS: Among the 110 SMCs, 79 (71.8%) were de novo, 24 (21.8%) were familial, and the origin was undetermined in 7 cases. Fifty-eight of the SMCs originated from nonacrocentric chromosomes and 52 SMCs were derived from acrocentric chromosomes, with 27 originating from chromosome 15. Twenty-two of the SMCs from chromosome 15 did not contain the Prader-Willi/Angelman syndrome critical region, and uniparental disomy was ruled out in 19/19 cases. Clinical information ranging from birth to 4 years was obtained for 46 de novo cases with nonchromosome-15-derived SMCs. Of these cases, 11/11 acrocentric SMCs resulted in normal phenotype. In contrast, 4/23 cases with single nonacrocentric SMCs and 3/5 cases with two or more SMCs resulted in an abnormal phenotype. CONCLUSIONS: Our data suggests an overall low risk for acrocentric SMCs and a higher risk for nonacrocentric SMCs. Phenotypes associated with markers derived from some specific chromosomes are also discussed.

Trisomy recurrence: a reconsideration based on North American data.

Few reliable data exist concerning the recurrence risk for individual trisomies or the risk for recurrence of trisomy for a different chromosome. We collected records from two sources: (1) prenatal diagnoses performed at the Hopital Sainte-Justine in Montreal and (2) karyotype analyses performed at Genzyme. Using the standardized morbidity ratio (SMR), we compared the observed number of trisomies at prenatal diagnosis with the expected numbers, given maternal age-specific rates (by single year). SMRs were calculated both for recurrence of the same trisomy (homotrisomy) and of a different trisomy (heterotrisomy). After all cases with an index trisomy 21 were combined, the SMR for homotrisomy was 2.4 (90% CI 1.6-3.4; P=.0005). For women with both the index trisomy and subsequent prenatal diagnosis at age <30 years, the SMR was 8.0; it was 2.1 for women with both pregnancies at age >/=30 years. For the other index viable trisomies (13, 18, XXX, and XXY) combined, the SMR for homotrisomy was 2.5 (90% CI 0.7-8.0). For heterotrisomy, the SMR after an index trisomy 21 was 2.3 (90% CI 1.5-3.8, P=.0007); the SMR did not vary with maternal age at the first trisomy. When all cases with index viable trisomies were combined, the SMR for heterotrisomy was 1.6 (90% CI 1.1-2.4; P=.04). For prenatal diagnoses following a nonviable trisomy diagnosed in a spontaneous abortion (from Genzyme data only), the SMR for a viable trisomy was 1.8 (90% CI 1.1-3.0; P=.04). The significantly increased risk for heterotrisomy supports the hypothesis that some women have a risk for nondisjunction higher than do others of the same age.

Partial duplication 2p as the sole abnormality in two cases with anencephaly.

Anencephaly/NTD has been observed in aneuploid and non-aneuploid individuals. We present two cases of anencephaly diagnosed prenatally with partial duplication of the short arm of chromosome 2 as the sole abnormality. The absence of aneuploidy involving other regions of the genome in these cases, further substantiates suggestions of the existence of a gene or genes on the short arm of chromosome 2 critical in the development of the central nervous system.

Residual risk for cytogenetic abnormalities after prenatal diagnosis by interphase fluorescence in situ hybridization (FISH).

Results from conventional cytogenetic studies on 21 609 amniotic fluid specimens were analyzed retrospectively to determine the residual risk for a cytogenetic abnormality if interphase FISH, capable of only detecting aneuploidy for chromosomes 13, 18, 21, X and Y, was performed and did not reveal an abnormality. Detection rates (the probability of detecting a cytogenetic abnormality when an abnormality is present) and residual risks (the likelihood of a cytogenetic abnormality, in view of normal interphase FISH results) were calculated for the four major clinical indications for prenatal diagnosis (advanced maternal age, abnormal maternal serum screen indicating increased risk for trisomy 18 or trisomy 21, abnormal maternal serum screen indicating increased risk for neural tube defects and ultrasound abnormality). Differences in detection rates were observed to depend on clinical indication and presence or absence of ultrasound abnormalities. The detection rate ranged from 18.2 to 82.6% depending on the clinical indication. The detection rates of abnormalities significant to the pregnancy being evaluated (i.e. abnormalities excluding familial balanced rearrangements and familial markers) were between 28.6 and 86.4%. The presence of ultrasound abnormalities increased the detection rate from 72.2 to 92.5% for advanced maternal age and from 78.6 to 91.3% for abnormal maternal serum screen, indicating increased risk for trisomy 18 or trisomy 21. With regard to residual risk, the risk for a clinically significant abnormality decreased from 0.9-10.1%, prior to the interphase FISH assay, to a residual risk of 0.6-1.5% following a normal interphase FISH result in the 4 groups studied. Providing patients with detection rates and residual risks, most relevant to their situation (clinical indication and presence or absence of ultrasound abnormality) during counseling, could help them better understand the advantages and limitations of interphase FISH in their prenatal diagnostic evaluation.

A t(4;11)(q21;p15) in a case of T-cell lymphoma and a case of acute myelogenous leukemia.

The translocation (4;11)(q21;p15) has been observed in acute lymphoblastic as well as acute myeloid leukemias (ALL and AML, respectively). We report the first case of T-cell lymphoma with t(4;11)(q21;p15) and a case of AML. The clinical history of and cytogenetics in the latter is suggestive of a secondary leukemia; his karyotype revealed emergence of a t(3;11)(q21;q13) in addition to the t(4;11). Previously reported cases with t(4;11)(q21;p15) are reviewed, clinical and morphological characteristics of cases with t(4;11)(q21;q23) and t(4;11)(q21;p15) are compared, and chromosome abnormalities involving the NUP98 gene in hematologic malignant disorders are reviewed.

Prenatal diagnosis of 45,X and 45,X mosaicism: the need for thorough cytogenetic and clinical evaluations.

OBJECTIVES: Mosaicism involving a 45,X cell line is relatively common in prenatal diagnosis. In prenatally diagnosed cases, the prognosis of non-mosaic 45,X and 45,X/46,XY mosaicism are different. Therefore, accurate identification of a cell line containing Y chromosome is critical for genetic counseling and postnatal management. METHODS: We investigated the ultrasound findings and outcomes of pregnancies with a 45,X cell line identified during mid-trimester cytogenetic analysis. RESULTS: A total of 105 cases were found to have a 45,X cell line by standard cytogenetic analysis. Seventy-four cases were found to have non-mosaic 45,X at initial diagnosis. Of these 74 cases, 68 had abnormal ultrasound findings that were characteristic of Turner syndrome. Of the six cases with normal ultrasound findings, ultrasound examination was normal with male genitalia identified in three cases. Thorough cytogenetic and fluorescent in situ hybridization (FISH) analysis identified Y chromosome material in all three cases, one with a dicentric Y;14 chromosome and the other two cases with a marker chromosome containing Sex-determining Region (SRY) material in a small portion of the cells. In contrast, in 31 cases with a mosaic 45,X karyotype, ultrasound abnormality was identified only in one case. CONCLUSIONS: The present data suggest the need for follow-up ultrasound examination and thorough cytogenetic and molecular analysis for Y chromosome material in 45,X cases with normal ultrasound findings.