Use Of Karyotyping Research Articles

Role of Conventional Cytogenetics and FISH in the Laboratory Work Up of Plasma Cell Dyscrasias

AbstractPlasma cell dyscrasias are a heterogeneous group of neoplasms characterized by abnormal proliferation of plasma cells with or without over production of monoclonal immunoglobulins. Chromosomal abnormalities are acquired either early in the course of the disease or during disease progression. Plasma cell dyscrasias are categorized into multiple cytogenetic subtypes that form an integral component of risk-stratified treatment protocols. The primary genetic events are IgH gene translocations and non-random gains of chromosomes 3/5/7/9/11/15/19 and or 21. The secondary genetic events consist of chromosome 1 abnormalities (1p deletion and 1q gain or amplification), deletion 17p/TP53, deletion 13q, and MYC gene rearrangements. Plasma cells being at the end of differentiation spectrum of B cells, have low proliferative potential precluding the use of karyotyping in identification of chromosomal abnormalities. Analysis of enriched plasma cells using interphase fluorescent in situ hybridization (FISH) is the technique of choice for identifying these abnormalities. It is essential to enrich plasma cells before the FISH analysis, and numerous plasma cell enrichment techniques have been described. In the paper, we review the cytogenetic approach to identify clinically significant genetic aberrations including the effective use of FISH panels and plasma cell enrichment techniques.

Comparison of the combined use of CNV-seq and karyotyping or QF-PCR in prenatal diagnosis: a retrospective study

To elevate the accuracy of diagnostic results, CNV-seq is usually performed simultaneously with karyotyping or QF-PCR. Although several studies have investigated the performance of the combined use of CNV-seq with karyotyping or QF-PCR, there have been no reports focusing on the comparison of these 2 diagnostic strategies. In our study, 2507 pregnant women were included to investigate these 2 strategies. The detection rates of foetal genetic abnormalities and turnaround time were compared between these 2 groups. Moreover, the detection rates of foetal genetic abnormalities in different indications were analyzed. Our results unveiled that the detection rates of numerical chromosomal abnormalities were nearly the same in these 2 groups. In addition to numerical chromosomal abnormalities, 39 balanced karyotypic changes and chromosome polymorphisms were detected via the combined use of karyotyping and CNV-seq. Further investigation revealed that the vast majority of these karyotypic changes were inherited from parents. Compared with the karyotyping group, the combination of QF-PCR and CNV-seq reduced the reporting time from 31.593 ± 4.944 days to 11.460 ± 4.894 days. Meanwhile, NIPT, maternal serum screening and ultrasound scan significantly improved the detection of foetal genetic abnormalities. In conclusion, our results revealed that parental karyotyping is a useful supplementary method for CNV-seq and systematic prenatal examinations improved the detection of foetal genetic defects.

Combined use of karyotyping and copy number variation sequencing technology in prenatal diagnosis.

Karyotyping and genome copy number variation sequencing (CNV-seq) are two techniques frequently used in prenatal diagnosis. This study aimed to explore the diagnostic potential of using a combination of these two methods in order to provide a more accurate clinical basis for prenatal diagnosis. We selected 822 pregnant women undergoing amniocentesis and separated them into six groups according to different risk indicators. Karyotyping and CNV-seq were performed simultaneously to compare the diagnostic performance of the two methods. Among the different amniocentesis indicators, abnormal fetal ultrasounds accounted for 39.29% of the total number of examinees and made up the largest group. The abnormal detection rate of non-invasive prenatal testing (NIPT) high risk was 37.93% and significantly higher than the other five groups (P<0.05). The abnormal detection rate of mixed indicators was significantly higher than the history of the adverse reproductive outcomes group (P = 0.0151). The two methods combined found a total of 119 abnormal cases (14.48%). Karyotyping detected 57 cases (6.93%) of abnormal karyotypes, 30 numerical aberrations, and 27 structural aberrations. CNV-seq identified 99 cases (12.04%) with altered CNVs, 30 cases of chromosome aneuploidies, and 69 structural aberrations (28 pathogenic, eight that were likely pathogenic, and 33 microdeletion/duplication variants of uncertain significance (VUS)). Thirty-seven cases were found abnormal by both methods, 20 cases were detected abnormally by karyotyping (mainly mutual translocation and mostly balanced), and 62 cases of microdeletion/duplication were detected by CNV-seq. Steroid sulfatase gene (STS) deletion was identified at chromosome Xp22.31 in three cases. Postnatal follow-up confirmed that babies manifested skin abnormalities one week after birth. Six fetuses had Xp22.31 duplications ranging from 1.5 Kb to 1.7 Mb that were detected by CNV-seq. Follow-up showed that five babies presented no abnormalities during follow-up, except for one terminated pregnancy due to a history of adverse reproductive outcomes. The combination of using CNV-seq and karyotyping significantly improved the detection rate of fetal pathogenic chromosomal abnormalities. CNV-seq is an effective complement to karyotyping and improves the accuracy of prenatal diagnosis.

Genetic Testing Protocol Reduces Costs and Increases Rate of Genetic Diagnosis in Infants with Congenital Heart Disease

Genetic testing is routinely performed on infants with critical congenital heart disease (CHD). This project reviewed the effect of implementing a genetic testing protocol in this population. Charts of infants with critical CHD were reviewed for genetic testing and results across two time periods: the time before implementation of a genetic testing protocol (pre-protocol) and the time after implementation (post-protocol). The use of karyotype, 22q11.2 Deletion testing, and chromosomal microarray were compared across these two time periods. Records of 891 infants were reviewed. 562 (63%) had at least one of the target genetic tests completed. During the pre-protocol time period, 66% of patients who had genetic testing underwent multiple tests versus 24% during the post-protocol time period (p < 0.01). The rate of patients who underwent genetic testing increased from 60% in the pre-protocol time period to 77% in the post-protocol time period (p < 0.01). The rate of diagnosis of genetic conditions during the pre-protocol period was 26% versus 36% during the post-protocol period (p = 0.01). There was a reduction in cost to patients by $5105.59 per diagnosis during the post-protocol period. Patients with critical CHD in the post-protocol period were less likely to undergo multiple genetic tests and more likely to have a diagnosis of genetic disease. In addition there was a significant reduction in cost per diagnosis during the post-protocol time period. Genetic testing protocols for infants with critical CHD promoted more efficient use of genetic testing and increased the rate of diagnosis of genetic conditions in this population.

A fetus with de novo 2q33.2q35 deletion including MAP2 with brain anomalies, esophageal atresia, and laryngeal stenosis

Deletions of the long arm of chromosome 2 are rare. Few cases of interstitial deletions of the 2q33q35 region have been reported. Individuals with deletions in this region have growth retardation, psychomotor retardation, micrognathia, microcephaly, and apparently low-set ears. We describe a female fetus with a de novo deletion of 2q33.2 to q35 with delayed gyral formation with widespread neuronal heterotopia of the white matter, small cerebellum, esophageal atresia, laryngeal stenosis, micrognathia, and intrauterine growth retardation. With the use of karyotyping and high-resolution array comparative genomic hybridization the boundaries and gene content of the deletion were identified. Our aim was to determine whether a candidate gene for the brain phenotype was present in the deletion. By this means and based on literature we pinpointed the microtubule associated gene MAP2 as a candidate for the brain anomalies.

Prevalencia y Caracterización de los Recién Nacidos con Anomalías Craneofaciales en el Instituto Materno Infantil de Bogotá

Determining the frequency and characteristics of newborn suffering craniofacial abnormalities who were attending the Instituto Materno Infantil (IMI) in Bogotá. Data was gathered regarding the newborn suffering such alterations who attended IMI from March 1st 2000 to August 15th 2001. The variables analysed were: being born in or having been remitted to the IMI, social strata, origin, general and specific risk factors, gender, correlation between weight and gestational age, clinical and aetiological diagnosis of the anomaly, karyotype and condition on leaving IMI. There was 2.7% prevalence for congenital defects and 0.6% for craniofacial abnormalities. 69% of the 52 patients had specific risk factors, 38% had been preterm, 33% had suffered retarded intra-uterine growth, 65% had cleft palates, 55.8% multiple abnormalities and 46% syndromes. Aetiological diagnosis was established in 38%; 12% had chromosomopathy. Eighteen children (35%) died, death being attributed to their defect in 13 of them, six by chromosomopathy. This study revealed the use of karyotype in making an aetiological diagnosis and determining prognosis. Mortality for the group suffering craniofacial abnormalities was threefold that of other hospitalised neonatal patients. Significant statistical association was shown between mortality and preterm condition, retarded growth, chromosomopathy and a diagnosis of multiple defects and/or syndromes. Prematurity, retarded growth, multiple defects, syndrome diagnosis and chromosomopathy revealed a mortality risk profile.

Chromosomal abnormalities in bronchial epithelium from smokers, nonsmokers, and lung cancer patients

The identification of individuals who are at greatest risk of developing lung cancer would greatly improve diagnosis and possibly lead to early treatment. To study the use of karyotypes for this purpose, we used short-term human bronchial epithelial (hBE) cell cultures from nonsmokers, smokers, and lung cancer patients. Twenty-five metaphases were scored for hBE cell cultures obtained from 32 patients: 8 were nonsmokers, and 24 had a history of smoking (of whom 11 had had lung cancer surgery). The number of abnormal metaphases ranged from 0 to 4 per cell culture. No overall differences in the number of abnormal metaphases were observed between nonsmokers and smokers or between lung cancer patients and non–lung cancer patients. The most commonly observed abnormalities were structural changes in chromosome 1 (six cultures), loss of chromosome 17 (six cultures), and trisomy of chromosome 20 (three cultures). These specific alterations were found almost exclusively in patients with a history of tobacco smoking. The results did not indicate that general chromosomal abnormalities are a useful marker for tobacco smoke exposure or cancer risk.

Use of karyotyping, FISH and CGH for characterization of genome imbalances in tumor cells

Use of karyotyping, FISH and CGH for characterization of genome imbalances in tumor cells

The use of karyotyping in the systematics of yeasts.

The use of electrophoretic karyotyping in systematics of yeasts is discussed. New data are provided on the karyotypes of the medically important fungi Hortaea werneckii, Filobasidiella (= Cryptococcus) neoformans, and Malassezia species. Hortaea werneckii has twelve to eighteen bands of chromosomal DNA, ranging in size between 500 and 2300 kb. The karyotypes of Filobasidiella neoformans consist of seven to fourteen bands of chromosomal DNA. The varieties neoformans and bacillispora cannot be separated by their karyotypes, and no obvious correlation was found with serotypes, geography or habitat. All strains of Malassezia pachydermatis studied have similar karyotypes consisting of five bands, whereas in M. furfur, four different karyotypes are prevalent. However, each of these karyotypes is stable.

Avoidance of emergency surgery in newborn infants with trisomy 18

Trisomy 18 (Edwards' syndrome) presents with characteristic external features as well as life-threatening abnormalities; many of these abnormalities require surgical correction during the neonatal period. Children with trisomy 18 have a very short life expectancy, and all long-term survivors have severe mental retardation. Difficult medical and ethical issues arise over whether or not to institute treatment when a newborn infant with suspected trisomy 18 has a life-threatening anomaly. We studied the policy of treatment in seven patients with clinical Edwards' syndrome. For three, the period of uncertainty was shortened because trisomy 18 was rapidly diagnosed by karyotyping of a bone-marrow aspirate. Four of the patients underwent surgery before the diagnosis of trisomy 18 was confirmed by routine karyotyping in lymphocytes; karyotyping in bone marrow might have allowed invasive treatment to be avoided in three of these. Rapid confirmation of clinically suspected Edwards' syndrome is very important because surgery may then be withheld. A newborn infant with trisomy 18 should be considered as a patient with a hopeless outlook who ought not to be subjected to invasive procedures. The decision to withdraw or withhold treatment should be discussed frankly with the parents. The period of uncertainty can be reduced to a minimum by the use of karyotyping in bone marrow.

Equine cytogenetics: role in equine veterinary practice.

The prognostic use of karyotyping in equine breeding has been recommended since 1976. Specimens used and laboratory methods are described. The system of karyotype evaluation is explained together with a glossary of terms. The principal aberrations in horses are defined. The present state of knowledge in cytogenetics in horses is reviewed dealing with infertility in the mare, where sex chromosomes give clear indication of problems; the situation with respect to anomalies found in stallions and hermaphroditism is explained coupled with recent concepts of chromosomal roles in reproduction. The future potential for the application of cytogenetics in equine practice is explained in regard to the advanced techniques and knowledge in the human parallel field. It is concluded that karyotyping is an essential tool in the evaluation of reproductive problems in practice and should be used more frequently in future.

The Chromosome Karyotype in Estimation of Lineage Relationships

Atchley, William R. (Dept. of Entomology, Univ. of Kansas, Lawrence, Kans. 66044)1 1972. The Chromosome Karyotype in Estimation of Lineage Relationships. Syst. Zool., 21:199-209.-The validity of phylogenetic speculations based on chromosome number and morphology alone is examined. Karyotypic attributes are examined by numerical phenetic methods in two groups of organisms where lineage relationships have been extensively studied by experimental methods. The results illustrate the inaccuracies of karyotypic data alone in inferring lineage relationships when intergenomic homologies are not available and the mechanisms of chromosomal change and direction of aneuploidy unknown. With the great proliferation of interest in chromosomal cytology by zoologists in recent years, increasing use has been made of karyotypes to infer taxonomic relationship and phylogeny. Cytological data have been used at varying levels of sophistication. Many botanists and insect geneticists have applied the truly cytogenetic approach of artificial hybridization and subsequent chromosomal analyses to gain evidence of genetic differentiation among taxa. At the other end of the spectrum, many practitioners of what might be termed have often been satisfied to simply compare different taxa on the basis of chromosome number and morphology and then speculate on genetic divergence. The use of chromosome number and morphology alone for determination of lineage relationships is suspect, since one is unable to determine chromosomal homologies in different genomes, the mechanisms involved in changes in chromosomal morphology are unknown as is the direction of aneuploidy to name some of the more outstanding problems. Further, it is intuitively obvious that in cases where the chromosomes of different genomes cannot be homologized, the degree of accuracy of the results is inversely proportional to the chromosome number. 'Present address: Dept. of Biology, Texas Tech University, Lubbock, Texas 79409. In spite of these serious shortcomings, many workers e.g., Gorman (1970), Cole (1970), Bogart (1970), Nadler (1966) and Liapunova and Vorontosov (1970) to name only a few, have used chromosome number and morphology to draw detailed conclusions about genetic divergence in various groups of vertebrates. Accurate information on homology of chromosomes in different genomes is mandatory if accurate conclusions are to be reached concerning the direction of chromosomal change. However, definitive proof of chromosomal homology, the direction of aneuploidy, etc., can generally be obtained only by experimental hybridization or, in a limited number of cases, by autoradiography. The latter technique is useful to show synchronous or asynchronous labeling patterns where translocations have occurred. Jackson (1971) has reviewed several new techniques for chromosomal analysis which show considerable promise in overcoming the above mentioned problems in organisms where hybridization is difficult or impossible. To my knowledge, however, none of these have been applied in karyotype systematics studies. The above statements and those throughout the remainder of the paper regarding the use of karyotypes relate to typical somatic chromosomes and do not necessarily hold for polytene chromosomes. In spite of the wide application of karyo-

Karyotypes and Karyotypic Variation of North American Vespertilionid Bats

Karyotypes of 32 species of North American vespertilionid bats are described. Individual, population, subspecific, specific, and generic karyotype variation are discussed. The use of karyotypes as a taxonomic tool and phylogenetic indicator in bats is discussed.