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Chromosomal evolution in the lizard genus Varanus (reptilia)

King M, King D

Aust. J. Biol. Sci., 1975 Feb;28(1):89-108.
PMID: 1164258

The karyotypes have been determined of 16 of the 32 species of the genus Varanus, including animals from Africa, Israel, Malaya and Australia. A constant chromosome number of 2n = 40 was observed. The karyotype is divided into eight pairs of large chromosomes and 12 paris of microchromosomes. A series of chromosomal rearrangements have become established in both size groups of the karyotype and are restricted to centromers shifts, probably caused by pericentric inversion. Species could be placed in one of six distinct karyotype groups which are differentiated by these rearrangements and whose grouping does not always correspond with the current taxonomy. An unusual sex chromosome system of the ZZ/ZW type was present in a number of the species examined. The evolutionary significance of these chromosomal rearrangements, their origin and their mode of establishment are discussed and related to the current taxonomic groupings. The most likely phylogenetic model based on chromosome morphology, fossil evidence and the current distribution of the genus Varanus is presented.

Matched MeSH terms: Karyotyping
Fulltext Karyotype pattern and maternal age distribution in down syndrome patients analyzed at Human Genome Centre, University Sains Malaysia, Kelantan

Siti Mariam I, Suhaida MA, Tarmizi AB, Norhasimah M, Nor Atifah MA, Kannan, T. P., et al.

Buletin Persatuan Genetik Malaysia, 2006;12(1):6-9.
MyJurnal

Down Syndrome (DS), is a complex genetic disease resulting from the presence of 3 copies of chromosome 21. It is the most common autosomal abnormality among live births and the most commonly recognized genetic cause of mental retardation. The only well established risk factor for DS is advanced maternal age. The Human Genome Center , University Sains Malaysia, Kelantan has been carrying out cytogenetic studies in DS patients. Here we, report the karyotype pattern of Down Syndrome patients in correlation with maternal age, among referral cases to our Center.

Matched MeSH terms: Karyotyping
Down syndrome as a result of de novo robertsonian translocation involving chromosome 14 and 21: a case report

Norhasimah, M.M., Ahmad Tarmizi, A.B., Azman, B.A., Zilfalil, B.A., Ankathil, R.

Malaysian Journal of Paediatrics and Child Health, 2007;15(1):46-49.
MyJurnal

Generally, the karyotype profile of Down Syndrome has been reported to be full trisomy 21 in 92% of patients, mosaic trisomy 21 in 4% of patients and translocation involving chromosome 21 in 4% of patients in most of the population groups worldwide. But, karyotype analysis of 149 DS patients at the Human Genome Center, USM, during the past five years revealed that free trisomy accounted for 94.6%, mosaic trisomy 21 for 4.7% and translocation involving chromosome 21 in 0.7% of the Down Syndrome etiology in North East Malaysian population, indicating a low frequency of translocation DS in this region. Here, we report one case of translocation Down Syndrome encountered during karyotype analysis of 149 DS cases. Karyotype showed a robertsonian translocation where an entire extra chromosome 21 was attached to the centromere of one of the chromosome 14, resulting in a derivative chromosome 14 with attached chromosome 21. Karyotype analysis of the parents revealed a normal 46,XY pattern for father and 46,XX pattern for mother indicating that this robertsonian translocation had arisen de novo either prior to or at conception.

Matched MeSH terms: Karyotyping
Fulltext Microarray-Based Genomic Analysis Identifies Germline and Somatic Copy Number Variants and Loss of Heterozygosity in Acute Myeloid Leukaemia

Ambayya, Angeli, Sasmita, Andrew Octavian, Zainina Seman, Chang, Kian Meng, Sathar, Jameela, Yegappan, Subramanian, et al.

Malaysian Journal of Medicine and Health Sciences, 2018;14(103):1-14.
MyJurnal

Insights into molecular karyotyping using comparative genomic hybridization (CGH) and single nucleotide polymorphism (SNP) arrays enable the identification of copy number variations (CNVs) at a higher resolution and facilitate the detection of copy neutral loss of heterozygosity (CN-LOH) otherwise undetectable by conventional cytogenetics. The applicability of a customised CGH+SNP 180K DNA microarray in the diagnostic evaluation of Acute Myeloid Leukaemia (AML) in comparison with conventional karyotyping was assessed in this study. Methods: Paired tumour and germline post induction (remission sample obtained from the same patient after induction) DNA were used to delineate germline variants in 41 AML samples and compared with the karyotype findings. Results: After comparing the tumour versus germline DNA, a total of 55 imbalances (n 5-10 MB = 21, n 10-20 MB = 8 and n >20 MB = 26) were identified. Gains were most common in chromosome 4 (26.7%) whereas losses were most frequent in chromosome 7 (28.6%) and X (25.0%). CN-LOH was mostly seen in chromosome 4 (75.0%). Comparison between array CGH+SNP and karyotyping revealed 20 cases were in excellent agreement and 13 cases did not concord whereas in 15 cases finding could not be confirmed as no karyotypes available. Conclusion: The use of a combined array CGH+SNP in this study enabled the detection of somatic and germline CNVs and CN-LOHs in AML. Array CGH+SNP accurately determined chromosomal breakpoints compared to conventional cytogenetics in relation to presence of CNVs and CN-LOHs.

Matched MeSH terms: Karyotyping
Fulltext Chromosomal abnormalities and reproductive outcome in Malaysian couples with miscarriages

Pal S, Ma SO, Norhasimah M, Suhaida MA, Siti Mariam I, Ankathil R, et al.

Singapore Med J, 2009 Oct;50(10):1008-12.
PMID: 19907893

This study was done to determine the prevalence of chromosomal abnormalities and the subsequent reproductive outcome in couples who had two or more miscarriages.

Matched MeSH terms: Karyotyping
Fulltext True hermaphrodite--a case report

Yip CH, Pathmanathan R

Singapore Med J, 1996 Feb;37(1):117-8.
PMID: 8783930

A case report of a male true hermaphrodite with 46XX/46XY karyotype is presented. He was first diagnosed at the age of 9 years when he presented with hypospadias and a left undescended testis. He was lost to follow-up until he presented at the age of 23 years with bilateral gynaecomastia. A hormonal profile showed a low testosterone level, while a seminal assay showed very few sperms. However he claimed to be sexually active. A year later, after he got married, he began to complain of impotence. A review of the condition is presented.

Matched MeSH terms: Karyotyping
Fulltext Two cases of deletion 5p syndrome: one with paternal involvement and another with atypical presentation

Azman BZ, Akhir SM, Zilfalil BA, Ankathil R

Singapore Med J, 2008 Apr;49(4):e98-e100.
PMID: 18418516

We report two cases of deletion 5p or cri du chat syndrome (CdCS) with different presentations and risks of transmission: one case with paternal chromosome 5 involvement and another, a de novo case with atypical clinical presentation. Cytogenetic analysis was performed on the two cases and their parents. GTG-banded karyotype analysis of Cases 1 and 2 revealed abnormal 46,XY,del(5)(p13-15) male karyotypes. For Case 1, the mother showed normal female karyotype while the father showed an abnormal karyotype involving a balanced translocation 46,XY,t(5;10)(p13;p15). For Case 2, however, both parents showed a normal karyotype pattern. In Case 1, the clinical features, particularly the distinct facial phenotype in combination with a characteristic cat-like cry and hypotonia, aided in the diagnosis at birth and the karyotype analysis was resolutive. The boy in Case 2 presented with atypical clinical features. Even though this patient had multiple syndromic features, the typical high pitched cat-like cry was not prominent. Instead, the patient manifested persistent stridor (from day three of life), which might have prevented the clinician from suspecting CdCS at birth. However, when this patient was presented at seven months of age for cytogenetic analysis, a confirmatory diagnosis of CdCS was established. For children with congenital abnormalities, an early clinical diagnosis confirmed through cytogenetic and molecular investigations, is important for providing personalised diagnostic and prognostic evaluation, and also for genetic counselling on the reproductive risk, particularly for patients with parental chromosome translocation involvement.

Matched MeSH terms: Karyotyping
Fulltext Interstitial deletion of the distal long arm of chromosome 4, del (4)(q33-q35), in association with paternal balanced translocation

Mdzin R, Ko C, Abdul Latif Z, Zakaria Z

Singapore Med J, 2008 Nov;49(11):e336-9.
PMID: 19037546

Interstitial deletions of the long arm of chromosome 4 are rare. The deletions may occur at the proximal or the distal portions of the chromosome and different breakpoints may be involved. We report an interstitial deletion of 4q: 46XY der 4 (q28;q35) in a six-year-old boy with dysmorphic features associated with moderate mental retardation. Parental chromosomal analysis showed a balanced paternal translocation.

Matched MeSH terms: Karyotyping
Fulltext Abnormalities of chromosome 11Q in three cases of acute myeloid leukemia

Ten SK, Khor MK, Khalid H, Lin HP, Ng SC, Cheong SK, et al.

Singapore Med J, 1992 Apr;33(2):164-6.
PMID: 1621121

The haematological findings and case history of 3 patients with the association of acute myeloid leukemia and translocation involving the long arm of chromosome no. 11 are presented. The recipient chromosome for the translocated material from chromosome 11 differs in all the three cases being namely chromosomes 1, 10 and 17.

Matched MeSH terms: Karyotyping
Fulltext Prevalence of chromosomal anomalies of the mentally retarded--report of a study of 124 institutionalised children in Kuala Lumpur

Noor PJ, Chin YM, Ten SK, Hassan K

Singapore Med J, 1987 Jun;28(3):235-40.
PMID: 2958941

A cytogenetic survey 01 124 children in lour special schools for the mentally handicapped was carried out to determine the contribution of chromosomal abnormalities to the aetiology of mental retardation in these children. All the children were karyotyped employing the G·banding technique 01 43 (34.7%) with an abnormal chromosome complement, 40 had Down's Syndrome, and 3 had other chromosomal abnormalities, namely a translocation 1;17, a mosaic male/trisomy 18 and a Klinefelter's syndrome. Polymorphic variants involving chromosomes 1, 9, and 14 were also observed. Two other children showed variants of the Y chromosome (one a small Y and the other a metacentric Y). The possible contribution by these abnormal variants to mental retardation is discussed. Details of the abnormal cytogenetic findings are reported.

Matched MeSH terms: Karyotyping
Variation of C-bands in the chromosomes of several subspecies of Rattus rattus

Yosida TH, Sagai T

Chromosoma, 1975;50(3):283-300.
PMID: 1149576

All subspecies of black rats (Rattus rattus) used in the present study are characterized by having large and clear C-bands at the centromeric region. The appearance of the bands, however, is different in the subspecies. Chromosome pair No. 1 in Asian type black rats (2n=42), which are characterized by an acrocentric and subtelocentric polymorphism, showed C-band polymorphism. In Phillipine rats (R. rattus mindanensis) the pair was subtelocentric with C-bands, but in Malayan black rats (R. rattus diardii) it was usually acrocentric with C-bands. In Hong-Kong (R. rattus flavipectus) and Japanese black rats (R. rattus tanezumi) it was polymorphic with respect to the presence of acrocentrics with C-bands or subtelocentrics without C-bands. The other chromosomes pairs showed clear C-bands, but in Hong-Kong black rats the pairs No. 2 and 5 were polymorphic with and without C-bands. In Japanese black rats, 6 chromosome pairs (No. 3, 4, 7, 9, 11 and 13) were polymorphic in regard to presence and absence of C-bands, but the other 5 chromosome pairs (No. 2, 5, 6, 8 and 10) showed always absence of C-bands. Only pair No. 12 usually showed C-bands. C-bands in small metacentric pairs (No. 14 to 20) in Asian type black rats generally large in size, but those in the Oceanian (2n=38) and Ceylon type black rats (2n=40) were small. In the hybrids between Asian and Oceanian type rats, heteromorphic C-bands, one large and the other small, were observed. Based on the consideration of karyotype evolution in the black rats, the C-band is suggested to have a tendency toward the diminution as far as the related species are concerned.

Matched MeSH terms: Karyotyping
Fulltext Clinical Features of Girls with Turner Syndrome in a Single Centre in Malaysia

Lee YL, Wu LL

J ASEAN Fed Endocr Soc, 2019;34(1):22-28.
PMID: 33442133 DOI: 10.15605/jafes.034.01.05

Objectives: Diagnosis of Turner syndrome in Malaysia is often late. This may be due to a lack of awareness of the wide clinical variability in this condition. In our study, we aim to examine the clinical features of all our Turner patients during the study period and at presentation.
Methodology: This was a cross-sectional study. Thirty-four (34) Turner patients were examined for Turner-specific clinical features. The karyotype, clinical features at presentation, age at diagnosis and physiologic features were retrieved from their medical records.
Results: Patients with 45,X presented at a median age of 1 month old with predominantly lymphoedema and webbed neck. Patients with chromosome mosaicism or structural X abnormalities presented at a median age of 11 years old with a broader clinical spectrum, short stature being the most common presenting clinical feature. Cubitus valgus deformity, nail dysplasia and short 4th/5th metacarpals or metatarsals were common clinical features occurring in 85.3%-94.1% of all Turner patients. Almost all patients aged ≥2 years were short irrespective of karyotype.
Conclusion: Although short stature is a universal finding in Turner patients, it is usually unrecognised till late. Unlike the 45,X karyotype, non-classic Turner syndrome has clinical features which may be subtle and difficult to discern. Our findings underscore the importance of proper serial anthropometric measurements in children. Awareness for the wide spectrum of presenting features and careful examination for Turner specific clinical features is crucial in all short girls to prevent a delay in diagnosis.

Matched MeSH terms: Karyotyping
Fulltext 45,X/46,XY Mosaicism in an 18-year-old Girl with Primary Amenorrhea : A Case Report

Lau EYC, Fung YK

J ASEAN Fed Endocr Soc, 2020;35(1):114-117.
PMID: 33442178 DOI: 10.15605/jafes.035.01.19

45,X/46,XY mosaicism is a rare disorder with a wide heterogeneity in its manifestations. An 18-year-old girl was referred to the endocrine clinic for investigation of her primary amenorrhea. Clinical examination was unremarkable. Hormonal profile was consistent with primary ovarian insufficiency and human chorionic gonadotropin (hCG) stimulation did not show evidence of active testicular tissue. Karyotyping studies by G-banding revealed a 45,X/46,XY karyotype. She was diagnosed with mosaic Turner syndrome with Y chromosomal material and investigation was performed to identify the presence of male gonads due to the risk of gonadal malignancy. Magnetic resonance imaging (MRI) of the pelvis did not show evidence of gonads. Laparoscopic exploration was proposed but the patient and parents refused opting for conservative management. This case highlights the challenges in the management of this rare condition.

Matched MeSH terms: Karyotyping
Practical Considerations for Using RNA Sequencing in Management of B-Lymphoblastic Leukemia: Malaysia-Singapore Acute Lymphoblastic Leukemia 2020 Implementation Strategy

Ni Chin WH, Li Z, Jiang N, Lim EH, Suang Lim JY, Lu Y, et al.

J Mol Diagn, 2021 10;23(10):1359-1372.
PMID: 34365011 DOI: 10.1016/j.jmoldx.2021.07.013

Despite the immense genetic heterogeneity of B-lymphoblastic leukemia [or precursor B-cell acute lymphoblastic leukemia (B-ALL)], RNA sequencing (RNA-Seq) could comprehensively interrogate its genetic drivers, assigning a specific molecular subtype in >90% of patients. However, study groups have only started to use RNA-Seq. For broader clinical use, technical, quality control, and appropriate performance validation are needed. We describe the development and validation of an RNA-Seq workflow for subtype classification, TPMT/NUDT15/TP53 variant discovery, and immunoglobulin heavy chain (IGH) disease clone identification for Malaysia-Singapore acute lymphoblastic leukemia (ALL) 2020. We validated this workflow in 377 patients in our preceding Malaysia-Singapore ALL 2003/Malaysia-Singapore ALL 2010 studies and proposed the quality control measures for RNA quality, library size, sequencing, and data analysis using the International Organization for Standardization 15189 quality and competence standard for medical laboratories. Compared with conventional methods, we achieved >95% accuracy in oncogene fusion identification, digital karyotyping, and TPMT and NUDT15 variant discovery. We found seven pathogenic TP53 mutations, confirmed with Sanger sequencing, which conferred a poorer outcome. Applying this workflow prospectively to the first 21 patients in Malaysia-Singapore ALL 2020, we identified the genetic drivers and IGH disease clones in >90% of patients with concordant TPMT, NUDT15, and TP53 variants using PCR-based methods. The median turnaround time was 12 days, which was clinically actionable. In conclusion, RNA-Seq workflow could be used clinically in management of B-cell ALL patients.

Matched MeSH terms: Karyotyping/methods
Refractory acute monoblastic leukaemia with low hypodiploidy

Lum SH, Chin TF, Lau KH, Yap TY, Rajagopal R, Ariffin H

Int J Hematol, 2014 Mar;99(3):215-6.
PMID: 24470150 DOI: 10.1007/s12185-014-1515-0
Matched MeSH terms: Karyotyping/methods
Fulltext Antigen expression pattern of acute promyelocytic leukaemia cases in Malaysia

Ambayya A, Zainina S, Salmiah MS, Sabariah MN

Med J Malaysia, 2014 Apr;69(2):64-9.
PMID: 25241814 MyJurnal

INTRODUCTION: Acute Promyelocytic Leukaemia (APL) is associated with devastating coagulopathy and life threatening condition which requires immediate medical attention. It is crucial to establish an expedited diagnosis as early therapeutic intervention has led to optimal patient management. In this study, we assessed the type and frequency of antigen expressions in APL and correlated these findings with genetic studies.

METHODS: Multiparametric immunophenotyping was performed on 30 samples and findings were correlated with karyotypes, FISH for t(15;17) translocation and RT-PCR for PML-RARΑ for detection of breakpoint cluster regions (bcr1,bcr2 and bcr3).

RESULTS: On SSC/CD45, APL cells displayed high to moderate SSC, with the expression of CD33 (100%), CD13 (96.8%), cMPO (71%) but lacked CD34 (3.2%) and HLA-DR (9.7%). Aberrant expression of CD4 was seen in 12.9% and CD56 in 6.5% of the cases. A significant association between cumulative aberrant antigen expression and bcr1 were observed bcr1 (X2(2) =6.833,p.05) and (X2(2)=4.599,p>.05) respectively.

CONCLUSIONS: Flow cytometry is a rapid and effective tool in detecting APL. It is interesting to note that there is significant association between cumulative aberrant antigen expression and genotype analysis. Further validation is required to corroborate this relationship.

Matched MeSH terms: Karyotyping
Development and characterization of a cell line TTCF from endangered mahseer Tor tor (Ham.)

Yadav K, Lakra WS, Sharma J, Goswami M, Singh A

Fish Physiol Biochem, 2012 Aug;38(4):1035-1045.
PMID: 22203177 DOI: 10.1007/s10695-011-9588-7

Tor tor is an important game and food fish of India with a distribution throughout Asia from the trans-Himalayan region to the Mekong River basin to Malaysia, Pakistan, Bangladesh and Indonesia. A new cell line named TTCF was developed from the caudal fin of T. tor for the first time. The cell line was optimally maintained at 28°C in Leibovitz-15 (L-15) medium supplemented with 20% fetal bovine serum (FBS). The propagation of TTCF cells showed a high plating efficiency of 63.00%. The cytogenetic analysis revealed a diploid count of 100 chromosomes at passage 15, 30, 45 and 60 passages. The viability of the TTCF cell line was found to be 72% after 6 months of cryopreservation in liquid nitrogen (-196°C). The origin of the cell lines was confirmed by the amplification of 578- and 655-bp sequences of 16S rRNA and cytochrome oxidase subunit I (COI) genes of mitochondrial DNA (mtDNA) respectively. TTCF cells were successfully transfected with green fluorescent protein (GFP) reporter plasmids. Further, immunocytochemistry studies confirm its fibroblastic morphology of cells. Genotoxicity assessment of H₂O₂ in TTCF cell line revealed the utility of TTCF cell line as in vitro model for aquatic toxicological studies.

Matched MeSH terms: Karyotyping
Taxonomic status of three types of Fejervarya cancrivora from Indonesia and other Asian countries based on morphological observations and crossing experiments

Kurniawan N, Djong TH, Islam MM, Nishizawa T, Belabut DM, Sen YH, et al.

Zoolog Sci, 2011 Jan;28(1):12-24.
PMID: 21186942 DOI: 10.2108/zsj.28.12

Although the crab-eating frog Fejervarya cancrivora is one of the most widely distributed species in Asian region, taxonomic relationships among different populations remain unclarified. In this study, we attempted to elucidate the taxonomic status of F. cancrivora from Indonesian and other Asian populations. Five populations of F. cancrivora from Selangor (Malaysia), Cianjur (Java, Indonesia), Trat (Thailand), Khulna (Bangladesh), and Makassar (Sulawesi, Indonesia) were morphologically observed and subjected to crossing experiments. Principal component and clustering analyses revealed that these five populations could be organized into three groups corresponding to three observed morphological types: a Selangor and Cianjur group (large-type), a Trat and Khulna group (mangrove-type), and a Makassar group (Sulawesi-type). The limited crossing experiments revealed that hybrids between Selangor females and Cianjur and Trat males developed normally, whereas hybrids between Selangor females and Khulna males showed incomplete gametic isolation. Histological observations of the testes of mature males revealed the presence of pycnotic nuclei in the hybrids between Selangor females and Khulna males in addition to normal bundles of spermatozoa. In contrast, no pycnotic nuclei were observed in the Selangor controls. Although meiotic metaphases in the controls were normal, those in hybrids showed several abnormalities, such as the appearance of univalents and an increase in rod-shaped bivalents. Based on our findings from the morphological observations and crossing experiments, we conclude that each of three identified types represents a distinct species. We propose that the large-type is F. cancrivora, the mangrove-type is F. moodiei, and the Sulawesi-type represents an undescribed species.

Matched MeSH terms: Karyotyping
Dermatoglyphics of Down's syndrome patients in Malays--a comparative study

Than M, Myat KA, Khadijah S, Jamaludin N, Isa MN

Anthropol Anz, 1998 Dec;56(4):351-65.
PMID: 10027045

There has been no recent report on the dermatoglyphics of the Malays (normal population as well as patients with Down's syndrome). A study on the frequencies of the dermal patterns (dermatoglyphics) of the digits, palms and hallucal areas was done therefore in 40 Malay patients with Down's syndrome and 200 unrelated normal controls. Only the patients with the standard 21 trisomy karyotype were included in the study. Comparison was made with the published data on studies done in various racial groups. Significant differences of the dermal patterns were found not only between the controls but also among patients of different races.

Matched MeSH terms: Karyotyping
Fulltext Supernumerary chromosomes in mosaic Turner syndrome

Thong MK, Manonmani V, Norlasiah IS

Med J Malaysia, 1996 Dec;51(4):487-90.
PMID: 10968041

The finding of a supernumerary or marker chromosome in a karyotype poses difficulty in genetic counselling. The true incidence and significance of this chromosomal aberration is unknown in Malaysia. We report two patients who presented with supernumerary chromosomes in mosaic Turner syndrome.

Matched MeSH terms: Karyotyping

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