Practice patterns of prenatal and perinatal testing in Canadian cytogenetics laboratories.

OBJECTIVE: To survey patterns of practice in Canadian cytogenetics laboratories and evaluate whether newer technologies have influenced testing algorithms for the detection of common aneuploidies and other genomic imbalances in the prenatal and perinatal settings. METHODS: Cytogenetics laboratories across Canada were invited to participate in two patterns-of-practice surveys: one in 2016 and one in 2019. They were asked to identify the prenatal and perinatal specimen types tested at their facility and which testing methods were used for initial testing and for follow-up. RESULTS: All clinical laboratories performing prenatal testing offer rapid aneuploidy detection (RAD). Most laboratories also offer microarray analysis. A positive result is either followed up by karyotyping or no further testing is performed. For prenatal samples, a negative result may be followed up by microarray or karyotyping and is dependent on the reason for referral. For perinatal samples, availability of microarray to follow up a negative result is increasing. CONCLUSIONS: Since 2016, the availability of RAD as a first-line test in Canadian cytogenetics laboratories remains consistent, while microarray has become the preferred follow-up testing method over traditional karyotyping following a normal RAD result. Despite a universal healthcare system, disparities in prenatal and perinatal cytogenetic testing algorithms are apparent.

Little evidence for switches to environmental sex determination and turnover of sex chromosomes in lacertid lizards.

Amniotes possess variability in sex determination, from environmental sex determination (ESD), where no sex chromosomes are present, to genotypic sex determination (GSD) with highly differentiated sex chromosomes. Some evolutionary scenarios postulate high stability of differentiated sex chromosomes and rare transitions from GSD to ESD. However, sex chromosome turnovers and two independent transitions from highly differentiated ZZ/ZW sex chromosomes to ESD were previously reported in the lacertid lizards. Here, we examined the homology of sex chromosomes in the wide phylogenetic spectrum of lacertids and their outgroups by comparing gene copy numbers between sexes in genes previously found to be Z-specific in some lacertids. Our current sampling covers 45 species from 26 genera including lineages supposed to possess a derived sex determining systems. We found that all tested lacertids share homologous differentiated ZZ/ZW sex chromosomes, which were present already in their common ancestor living around 85 million years ago. These differentiated sex chromosomes are not present in amphisbaenians and teiid lizards, the close relatives of lacertids. Our study demonstrates how inaccuracies in data can influence the outcome of phylogenetic reconstructions of evolution of sex determination, in this case they overestimated the number of shifts from GSD to ESD and the rate in turnovers of sex chromosomes.

Data-Driven Iterative Refinement of Bone Marrow Testing Protocols Leads to Progressive Improvement in Cytogenetic and Molecular Test Utilization.

OBJECTIVES: To determine the effect of iterative refinement of standard ordering protocols on test utilization and results for bone marrow biopsy specimens. METHODS: Eighteen months of test utilization and result data were used to revise the protocols that determine cytogenetic and molecular test selection on bone marrow specimens and then compared with data obtained following protocol revision. RESULTS: Revision of protocols resulted in reduction in total tests and associated charges, due to a decrease in tests both concordant and discordant with the protocols. These reductions only occurred in diseases for which revisions were made and were limited to cases in which reflex testing was performed. There was an increase in the fraction of positive tests, which was also limited to reflex testing. CONCLUSIONS: Data-driven iterative revision of protocols further improves test utilization and performance, while reducing cost. Analysis of testing data can be used to continuously improve test ordering decisions.

Non-invasive screening and rapid QF-PCR assay can greatly reduce the need for conventional cytogenetic analyses in prenatal diagnosis.

In 2004, the UK National Screening Committee suggested that rapid screening tests, such as fluorescence in-situ hybridization (FISH) and/or quantitative fluorescence PCR (QF-PCR), should replace prenatal diagnosis of Down syndrome performed by conventional karyotyping. However, doubts have been expressed that replacement of conventional cytogenetic investigations would result in a substantial number of infants affected by preventable handicaps. Based on a brief analysis of 28,000 prenatal tests performed in genetic units, this paper discusses the advantages of using QF-PCR. All normal fetuses were correctly diagnosed without false positive results and approximately 93% major chromosome disorders were detected by the molecular approach. The need for cytogenetic tests was thus greatly reduced, since pregnancy can be terminated, if necessary, without the need to confirm the results. A careful combination of accurately performed non-invasive ultrasound and maternal blood tests, eventually followed by QF-PCR, should reduce the need for conventional chromosome analyses.

Computer aided analysis of additional chromosome aberrations in Philadelphia chromosome positive acute lymphoblastic leukaemia using a simplified computer readable cytogenetic notation.

BACKGROUND: The analysis of complex cytogenetic databases of distinct leukaemia entities may help to detect rare recurring chromosome aberrations, minimal common regions of gains and losses, and also hot spots of genomic rearrangements. The patterns of the karyotype alterations may provide insights into the genetic pathways of disease progression. RESULTS: We developed a simplified computer readable cytogenetic notation (SCCN) by which chromosome findings are normalised at a resolution of 400 bands. Lost or gained chromosomes or chromosome segments are specified in detail, and ranges of chromosome breakpoint assignments are recorded. Software modules were written to summarise the recorded chromosome changes with regard to the respective chromosome involvement. To assess the degree of karyotype alterations the ploidy levels and numbers of numerical and structural changes were recorded separately, and summarised in a complex karyotype aberration score (CKAS). The SCCN and CKAS were used to analyse the extend and the spectrum of additional chromosome aberrations in 94 patients with Philadelphia chromosome positive (Ph-positive) acute lymphoblastic leukemia (ALL) and secondary chromosome anomalies. Dosage changes of chromosomal material represented 92.1% of all additional events. Recurring regions of chromosome losses were identified. Structural rearrangements affecting (peri)centromeric chromosome regions were recorded in 24.6% of the cases. CONCLUSIONS: SCCN and CKAS provide unifying elements between karyotypes and computer processable data formats. They proved to be useful in the investigation of additional chromosome aberrations in Ph-positive ALL, and may represent a step towards full automation of the analysis of large and complex karyotype databases.

A nonparametric Bayesian modeling approach for cytogenetic dosimetry.

In cytogenetic dosimetry, samples of cell cultures are exposed to a range of doses of a given agent. In each sample at each dose level, some measure of cell disability is recorded. The objective is to develop models that explain cell response to dose. Such models can be used to predict response at unobserved doses. More important, such models can provide inference for unknown exposure doses given the observed responses. Typically, cell disability is viewed as a Poisson count, but in the present work, a more appropriate response is a categorical classification. In the literature, modeling in this case is very limited. What exists is purely parametric. We propose a fully Bayesian nonparametric approach to this problem. We offer comparison with a parametric model through a simulation study and the analysis of a real dataset modeling blood cultures exposed to radiation where classification is with regard to number of micronuclei per cell.

Estudio citogenético en pacientes con leucemia mieloblástica aguda: Caracterización de grupos de riesgo por estudios cromosómicos / Cytogenetic study in patients with acute myeloblastic leukemia: Characterization of high risk groups by cytogenetic studies

Presentamos el estudio citogenético en 30 pacientes adultos en los que se diagnosticó leucemia mieloblástica aguda de novo, para caracterizar grupos de mayor riesgo en nuestra población. Los pacientes fueron tratados con esquemas conocidos "7 + 3" de daunorrubicina y arabinósido de citosina; así como ácido retinoico en los casos de M3. El cariotipo se realizó al momento del diagnóstico y en el seguimiento cada seis a ocho meses. Se observaron alteraciones cromosómicas en 90 por ciento de los casos, una incidencia mayor a la registrada en la literatura. Una respuesta clínica efectiva con periodos más largos de remisión y supervivencia se observó en los pacientes que tenían M2 con t(8;21), M4 con rearreglos de (16g) o cariotipo normal. En cambio, los pacientes con M3 y t(15;17) o los que presentan t(9;22), +8, o -7 tuvieron las peores respuestas, con menor tiempo de remisión y los más altos índices de mortalidad, por lo que deben considerarse de alto riesgo en nuestra población

Alteraciones citogenéticas en niños con leucemia aguda no linfoblástica / Cytogenetic defects in children with acute non-limphoblastic leukemia

Se realizó en 16 niños con leucemia aguda no linfoblástica estudio citogenético de la médula ósea por medio de dos métodos para la obtención de cariotipo para su análisis cromosómico: el método directo y el de cultivo de 48 horas. La investigación tuvo como objeto conocer las alteraciones citogenéticas en la población, debido al origen clonal de la enfermedad. Estas son útiles para valorar la remisión de la enfermedad y la respuesta al tratamiento, a la vez que permite dar un pronóstico

Prenatal cytogenetic diagnosis of the fragile X syndrome in amniotic fluid: calculation of accuracy.

We have completed over 350 prenatal diagnoses for the fragile X [fra(X)] syndrome using amniotic fluid, chorion villus specimen (CVS), fetal blood sampling and molecular methods. A total of 300 amniotic fluid specimens have been received for prenatal diagnosis of the fra(X) syndrome. There was a documented family history of fra(X) in 170/300 amniotic fluid cases, and 23/170 were correctly identified as cytogenetically fra(X) positive (16 male; 7 female). Three males were false-negative, and one female was fra(X) negative but identified as a probable carrier by RFLPs. No fra(X) positive or false-negative results were found in the absence of a fra(X) family history. Because the a priori risk for the fra(X) syndrome for each pregnancy was different and widely variable, the determination of the accuracy of the prenatal diagnosis results requires a consideration of these variables. On this basis, the calculated accuracy of prenatal cytogenetic diagnosis for the fra(X) syndrome is approximately 97%. This accuracy can be improved further with the simultaneous use of molecular methods, especially in view of recent developments.

Prenatal diagnosis of fragile X syndrome: results from parallel molecular and cytogenetic studies.

Since 1985, we have provided coordinated DNA-based and cytogenetic prenatal analysis for couples at risk for offspring afflicted with the fragile X [fra(X)] syndrome. To date, 40 pregnancies have been studied (22 males, 18 females). There were 5 males and 3 females identified to be at high risk by DNA but only 2 males and one female were demonstrated to be cytogenetically expressing the fra(X) prenatally. Of the other 3 males, one was a cytogenetic false negative (i.e. confirmed fra(X)+ at termination of pregnancy). The other 2 remain fra(X)- and are developing normally (undetected recombinants or non-penetrant male carriers). All fetuses at low risk were carried to term and are reported to be normal.