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Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers

Ngoot-Chin T, Zulkifli MA, van de Weg E, Zaki NM, Serdari NM, Mustaffa S, et al.

Planta, 2021 Feb 05;253(2):63.
PMID: 33544231 DOI: 10.1007/s00425-021-03567-7

MAIN CONCLUSION: Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts. Oil palm produces a quarter of the world's total vegetable oil. In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts of sequence information, allowing SNP discovery. High-capacity SNP genotyping platforms have been widely used for marker-trait association studies in oil palm. Besides genotyping, a SNP array is also an attractive tool for understanding aberrations in chromosome inheritance. Exploiting this, the present study utilized chromosome-wide SNP allelic distributions to determine the ploidy composition of over 1,000 oil palms from a commercial F1 family, including 197 derived from twin-embryo seeds. Our method consisted of an inspection of the allelic intensity ratio using SNP markers. For palms with a shifted or abnormal distribution ratio, the SNP allelic frequencies were plotted along the pseudo-chromosomes. This method proved to be efficient in identifying whole genome duplication (triploids) and aneuploidy. We also detected several loss of heterozygosity regions which may indicate small chromosomal deletions and/or inheritance of identical by descent regions from both parents. The SNP analysis was validated by flow cytometry and chromosome counts. The triploids were all derived from twin-embryo seeds. This is the first report on the efficiency and reliability of SNP array data for karyotyping oil palm chromosomes, as an alternative to the conventional cytogenetic technique. Information on the ploidy composition and chromosomal structural variation can help to better understand the genetic makeup of samples and lead to a more robust interpretation of the genomic data in marker-trait association analyses.

Matched MeSH terms: Chromosome Aberrations*
Supernumerary chromosomes in the black rat (Rattus rattus) and their distribution in three geographic variants

Yosida TH

Cytogenet. Cell Genet., 1977;18(3):149-59.
PMID: 862437

Supernumerary chromosomes have been examined in 352 black rats, covering three geographic variants, by use of conventional and C-band staining techniques. Metacentric supernumerary chromosomes, one to three in number, were found in Malayan black rats (Rattus rattus diardii), with 2n=42, in Indian black rats (R. rattus rufescens), with 2n=38, and in Ceylonese black rats (R. rattus kandianus), with 2n=40. The supernumeraries had similar morphology and stained heavily along their entire length by C-band staining. These findings suggested that the supernumeraries had originally developed in the Asian-type black rats and then were sequentially transmitted to the Ceylonese and Oceanian-type black rats, probably in southwestern Asia. A subtelocentric supernumerary chromosome found in one Japanese black rat seemed to have developed independently from the above metacentric supernumeraries.

Matched MeSH terms: Chromosome Aberrations*
Fulltext Dicentric assay technique for the assessment of whole body dose to low let radiation

Noriah Jamal, Noraisyah Mohd Yusof, Rahimah Abdul Rahim, Juliana Mahamad Napiah, Bo, Nelly Nai Lee, Yahaya Talib, et al.

Journal of Nuclear and Related Technologies, 2010;2010(1):77-83.
MyJurnal

For more than two decades, biodosimetry has been used in biomonitoring of occupational and envir onmental exposure to ionising radiation. Chromosome aberration analysis is a method used to dete ct unstable aberrations in the lymphocytes of irradiated personnel. The Malaysian National Biodosi metry Laboratory is a referance centre for activity relating to biodosimetry in the country. This pap er aims at presenting dicentric assay technique for the assessment of whole body dose to low LET ra diation at the Malaysian National Biodosimetry Laboratory.

Matched MeSH terms: Chromosome Aberrations
Cytogenetics analysis as the central point of genetic testing in acute myeloid leukemia (AML): a laboratory perspective for clinical applications

Rosli AA, Azlan A, Rajasegaran Y, Mot YY, Heidenreich O, Yusoff NM, et al.

Clin Exp Med, 2023 Aug;23(4):1137-1159.
PMID: 36229751 DOI: 10.1007/s10238-022-00913-1

Chromosomal abnormalities in acute myeloid leukemia (AML) have significantly contributed to scientific understanding of its molecular pathogenesis, which has aided in the development of therapeutic strategies and enhanced management of AML patients. The diagnosis, prognosis and treatment of AML have also rapidly transformed in recent years, improving initial response to treatment, remission rates, risk stratification and overall survival. Hundreds of rare chromosomal abnormalities in AML have been discovered thus far using chromosomal analysis and next-generation sequencing. As a result, the World Health Organization (WHO) has categorized AML into subgroups based on genetic, genomic and molecular characteristics, to complement the existing French-American classification which is solely based on morphology. In this review, we aim to highlight the most clinically relevant chromosomal aberrations in AML together with the technologies employed to detect these aberrations in laboratory settings.

Matched MeSH terms: Chromosome Aberrations
Clinical manifestations in trisomy 9

Kannan TP, Hemlatha S, Ankathil R, Zilfalil BA

Indian J Pediatr, 2009 Jul;76(7):745-6.
PMID: 19475342 DOI: 10.1007/s12098-009-0158-2

Complete trisomy 9 is a lethal diagnosis and most fetuses diagnosed thus die prenatally or during the early postnatal period and majority of such cases have been known to end in spontaneous abortion in the first trimester itself. One such rare survival of fetus ending in normal delivery and surviving until 20 days is reported here detailing the clinical manifestations of the child during the period of survival. The salient clinical features observed were small face, wide fontanel, prominent occiput, micrognathia, low set ears, upslanting palpebral fissures, high arched palate, short sternum, overlapping fingers, limited hip abduction, rocker bottom feet, heart murmurs and also webbed neck, characteristic of this trisomy 9 syndrome.

Matched MeSH terms: Chromosome Aberrations*
In vivo chromosome aberration test for hydroxyapetite in mice

Kannan TP, Nik Ahmad Shah NL, Azlina A, Samsudin AR, Narazah MY, Salleh M

Med J Malaysia, 2004 May;59 Suppl B:115-6.
PMID: 15468845

This study evaluates the cytotoxic and mutagenic effect of synthetic hydroxyapatite granules (source: School of Material and Mineral Resources Engineering, Universiti Sains Malaysia) in the bone marrow cells of mice. Mice are exposed to synthetic hydroxyapatite granules, the bone marrow cells are collected and observed for chromosome aberrations. No chromosome aberrations were noticed in the animals exposed to distilled water (negative control) and to the test substance, synthetic hydroxyapatite granules (treatment) groups. Chromosome aberrations were observed in the animals exposed to Mitomycin C (positive control group). There was no indication of cytotoxicity due to synthetic hydroxyapatite granules in the animals as revealed by the mitotic index. Hence, synthetic hydroxyapatite granules are considered non-mutagenic under the prevailing test conditions.

Matched MeSH terms: Chromosome Aberrations*
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: Chromosome Aberrations*
The chromosomes of four species of the nasuta complex of Drosophila. I. Chromosome maps and inversion polymorphism

Lambert DM

J Hered, 1976 3 1;67(2):92-8.
PMID: 5483

The salivary chromosomes of four species of the nasuta complex of Drosophila, D. sulfurigaster albostrigata, D, kohkoa, D. albomicans, and D. kepulauana were studied and chromosome maps of each species are presented; the maps of the latter three species are based on the map of D. sulfurigaster albostrigata. Three of the species D. sulfurigaster albostrigata, D. albomicans, and D. kohkoa were shown to be highly polymorphic for chromosomal inversions while the available evidence indicated that D. kepulauana is much less polymorphic. These facts are correlated with the geographic distribution of the species. Transitional homoselection has not been complete in the evolution of three of the species since D. sulfurigaster albostrigata, D. kohkoa, and D. albomicans have a number of naturally occurring polymorphisms in common.

Matched MeSH terms: Chromosome Aberrations*
Fulltext Down syndrome: multimodality imaging of associated congenital anomalies and acquired diseases

Tan AP

Med J Malaysia, 2013 Dec;68(6):482-9.
PMID: 24632922

Down syndrome (Trisomy 21) is the most common chromosomal abnormality among liveborn infants. It is the most frequent form of intellectual disability caused by a microscopically demonstrable chromosomal aberration. Management requires a multidisciplinary approach to the ongoing evaluation and monitoring for associated congenital anomalies and acquired disorders.Trisomy 21 is characterized by a variety of dysmorphic features, congenital anomalies and associated medical conditions. Knowledge of these associated conditions are important for clinicians involved in the management of these patients. Appropriate radiologic imaging with prompt, accurate interpretation plays an important role in the diagnosis and management of these diseases. The primary goal of this pictorial review is to unravel the radiological findings of these associated conditions.

Matched MeSH terms: Chromosome Aberrations
Fulltext Late presentation of turner syndrome and its complications

Huzairi Sani, Nada Syazana Zulkufli

Journal of Clinical and Health Sciences, 2018;3(2):51-55.
MyJurnal

Turner syndrome is one of the most common sex chromosome abnormalities with an estimated true prevalence of 1 in 2,000 in newborns. This case report is of a girl who presented to the adult endocrinologist at 16 years of age and subsequently diagnosed with Turner syndrome. Despite frequenting clinics for unrelated ailments, her short stature was overlooked hence not investigated for a causative pathology. The aim of this report is to explore the diagnostics of Turner syndrome, hormone treatments available and the importance of starting treatment early.

Matched MeSH terms: Sex Chromosome Aberrations
Fulltext A review on current status on cytogenetic biodosimetry methods for radiation dose assessment

Noriah Jamal, Bo, Nelly Nai Lee, Rahimah Abdul Rahim, Noraisyah Yusof, Yahaya Talib, Hasmadi Hassan, et al.

Journal of Nuclear and Related Technologies, 2009;2009(2):17-26.
MyJurnal

The blooming use of ionizing radiation in industry, research, agriculture, medicine and nuclear industry increases the risk of overexposure for radiation workers as well as members of the public. Ionizing radiation is a strong clastogen, causing chromosome breakage, and resulting in cytogenetic aberrations in exposed cells. Cytogenetic analysis of human blood lymphocytes has been widely used as the biological technique for quantifying radiation dose in man. In the investigation of radiation accident, it is important to estimate the dose absorbed by the exposed person in order for the attending medical doctor to plan for their therapy. This paper reviews the current status on cytogenetic biodosimetry methods for radiation dose assessment.

Matched MeSH terms: Chromosome Aberrations
Evaluation of the Oncomine Comprehensive Assay v3 panel for the detection of 1p/19q codeletion in oligodendroglial tumours

Ali RH, Alateeqi M, Jama H, Alrumaidhi N, Alqallaf A, Mohammed EM, et al.

J Clin Pathol, 2023 Feb;76(2):103-110.
PMID: 34489310 DOI: 10.1136/jclinpath-2021-207876

AIMS: Accurate assessment of 1p/19q codeletion status in diffuse gliomas is of paramount importance for diagnostic, prognostic and predictive purposes. While targeted next generation sequencing (NGS) has been widely implemented for glioma molecular profiling, its role in detecting structural chromosomal variants is less well established, requiring supplementary informatic tools for robust detection. Herein, we evaluated a commercially available amplicon-based targeted NGS panel (Oncomine Comprehensive Assay v3) for the detection of 1p/19q losses in glioma tissues using an Ion Torrent platform and the standard built-in NGS data analysis pipeline solely.
METHODS: Using as little as 20 ng of DNA from formalin-fixed paraffin-embedded tissues, we analysed 25 previously characterised gliomas for multi-locus copy number losses (CNLs) on 1p and 19q, including 11 oligodendrogliomas (ODG) and 14 non-oligodendroglial (non-ODG) controls. Fluorescence in-situ hybridisation (FISH) was used as a reference standard.
RESULTS: The software confidently detected combined contiguous 1p/19q CNLs in 11/11 ODGs (100% sensitivity), using a copy number cut-off of ≤1.5 and a minimum of 10 amplicons covering the regions. Only partial non-specific losses were identified in non-ODGs (100% specificity). Copy number averages of ODG and non-ODG groups were significantly different (p<0.001). NGS was concordant with FISH and was superior to it in distinguishing partial from contiguous losses indicative of whole-arm chromosomal deletion.
CONCLUSIONS: This commercial NGS panel, along with the standard Ion Torrent algorithm, accurately detected 1p/19q losses in ODG samples, obviating the need for specialised custom-made informatic analyses. This can easily be incorporated into routine glioma workflow as an alternative to FISH.

Matched MeSH terms: Chromosome Aberrations
Cytogenetics of ticks (Acari: Ixodoidea). 14. Chromosomes of nine species of Asian haemaphysalines

Oliver JH, Tanaka K, Sawada M

Chromosoma, 1974 May 10;45(4):445-56.
PMID: 4837734
Matched MeSH terms: Chromosome Aberrations
Fluorescence in situ hybridization analysis using PAX8- and PPARG-specific probes reveals the presence of PAX8-PPARG translocation and 3p25 aneusomy in follicular thyroid neoplasms

Chia WK, Sharifah NA, Reena RM, Zubaidah Z, Clarence-Ko CH, Rohaizak M, et al.

Cancer Genet. Cytogenet., 2010 Jan 1;196(1):7-13.
PMID: 19963130 DOI: 10.1016/j.cancergencyto.2009.08.001

At the present time, the differentiation between follicular thyroid carcinoma (FTC) and adenoma can be made only postoperatively and is based on the presence of capsular or vascular invasion. The ability to differentiate preoperatively between the malignant and benign forms of follicular thyroid tumors assumes greater importance in any clinical setting. The PAX8-PPARG translocation has been reported to occur in the majority of FTC. In this study, a group of 60 follicular thyroid neoplasms [18 FTC, 1 Hurthle cell carcinoma (HCC), 24 follicular thyroid adenomas (FTA), 5 Hurthle cell adenomas (HCA), and 12 follicular variants of papillary thyroid carcinomas (FV-PTC)] were analyzed to determine the prevalence of the PAX8-PPARG translocation by fluorescence in situ hybridization. The PAX8-PPARG translocation was detected in 2/18 FTC (11.1%). In addition, 2/18 (11.1%) FTC and 1/5 (20%) HCA showed 3p25 aneusomy only. The frequency of the translocation detected in the study was lower compared to the earlier studies conducted in Western countries. This might be attributed to the ethnic background and geographic location. Detection of either the PAX8-PPARG translocation or the 3p25 aneusomy in FTC indicates that these are independent genetic events. It is hereby concluded that 3p25 aneusomy or PAX8-PPARG translocation may play an important role in the molecular pathogenesis of follicular thyroid tumors.

Matched MeSH terms: Chromosome Aberrations*
Genotoxicity evaluation of dental restoration nanocomposite using comet assay and chromosome aberration test

Musa M, Ponnuraj KT, Mohamad D, Rahman IA

Nanotechnology, 2013 Jan 11;24(1):015105.
PMID: 23221152 DOI: 10.1088/0957-4484/24/1/015105

Nanocomposite is used as a dental filling to restore the affected tooth, especially in dental caries. The dental nanocomposite (KelFil) for tooth restoration used in this study was produced by the School of Dental Sciences, Universiti Sains Malaysia, Malaysia and is incorporated with monodispersed, spherical nanosilica fillers. The aim of the study was to determine the genotoxic effect of KelFil using in vitro genotoxicity tests. The cytotoxicity and genotoxicity of KelFil was evaluated using MTT assay, comet assay and chromosome aberration tests with or without the addition of a metabolic activation system (S9 mix), using the human lung fibroblast cell line (MRC-5). Concurrent negative and positive controls were included. In the comet assay, no comet formation was found in the KelFil groups. There was a significant difference in tail moment between KelFil groups and positive control (p < 0.05). Similarly, no significant aberrations in chromosomes were noticed in KelFil groups. The mitotic indices of treatment groups and negative control were significantly different from positive controls. Hence, it can be concluded that the locally produced dental restoration nanocomposite (KelFil) is non-genotoxic under the present test conditions.

Matched MeSH terms: Chromosome Aberrations*
Chromosome aberration test for hydroxyapatite in sheep

Kannan TP, Nik Ahmad Shah NL, Azlina A, Samsudin AR, Narazah MY, Salleh M

Med J Malaysia, 2004 May;59 Suppl B:168-9.
PMID: 15468871

The present study is aimed at finding the mutagenicity and cytotoxicity of dense form of synthetic hydroxyapatite (Source: School of Materials and Mineral Resources Engineering, Universiti Sains Malaysia) in the blood of sheep. The biomaterial was implanted in the tibia of Malin, an indigenous sheep breed of Malaysia. Blood was collected from the sheep before implantation of the biomaterial, cultured and a karyological study was made. Six weeks after implantation, blood was collected from the same animal, cultured and screened for chromosome aberrations. The mitotic indices and karyological analysis indicated that the implantation of synthetic hydroxyapatite (dense form) did not produce any cytotoxicity or chromosome aberrations in the blood of sheep.

Matched MeSH terms: Chromosome Aberrations*
Fulltext Trisomy X and myelodysplastic syndrome (MDS) with eosinophilia

Eusni, R.M.T., Leong, C.F., Salwa, S.

Malaysian Journal of Medicine and Health Sciences, 2012;8(2):65-67.
MyJurnal

We reported a young patient with myelodysplastic syndrome (MDS) with eosinophilia, in which her chromosomal analysis revealed the presence of trisomy X and a marker chromosome at chromosome 11. The technique used to detect the chromosomal abnormalities is a multicoloured –fluorescent in situ hybridization technique (M-FISH). Our observation suggested that these underlying chromosomal abnormalities were probably responsible for her development of MDS with eosinophilia.
Myelodysplastic syndrome (MDS) is a condition whereby there is ineffective production of haematopoietic stem cells and poor quality of cells produced. The cause can either be a primary bone marrow problem, de novo or therapy related. Most MDS cases are secondary rather than primary. Many chromosomal abnormalities have been found in cases of myelodysplastic syndrome. We described a case of MDS with eosinophilia in association with presence of trisomy X and a marker chromosome in chromosome 11.

Matched MeSH terms: Chromosome Aberrations; Sex Chromosome Aberrations
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: Chromosome Aberrations*
Fulltext Birth defects in Singapore: 1994-2000

Tan KH, Tan TY, Tan J, Tan I, Chew SK, Yeo GS

Singapore Med J, 2005 Oct;46(10):545-52.
PMID: 16172775

To study characteristics of birth defect cases among live births, stillbirths and abortions in Singapore between 1994 and 2000.

Matched MeSH terms: Chromosome Aberrations/statistics & numerical data
Fulltext In vivo anticlastogenic effect of silymarin from milk thistle Silybum marianum L

Anwar S, Madkor HR, Ahmed N, Wagih ME

Indian J Pharmacol, 2018 9 1;50(3):108-115.
PMID: 30166747 DOI: 10.4103/ijp.IJP_660_16

OBJECTIVE: Silymarin, extracted from the seeds of Silybum marianum L. (Milk thistle), is traditionally used for treating various illnesses such as diabetes, cancer, inflammation, hepatitis, liver cirrhosis, and renal problems. Acute cytotoxicity and genotoxicity studies have been reported with ambiguous outcomes; however, its relevant anticlastogenic potential is not yet evaluated. This study was aimed to evaluate in vivo subacute anticlastogenic properties of silymarin to validate its use as a medicinal agent.
MATERIALS AND METHODS: Silymarin was isolated from seeds of milk thistle. Various genotoxicity bioassays of silymarin were performed using mice. First, the bone marrow cell proliferation was estimated by calculating mitotic index. Second, the chromosomal abnormalities in mice bone marrow cells were studied. Third, micronucleated polychromatic erythrocytes (MPE) test and in vivo activation of sister chromatid exchanges (SCEs) were carried out in mice bone marrow cells. Finally, primary spermatocytes were analyzed to estimate genotoxic effect of silymarin on germ cells.
RESULTS: We found that silymarin is capable of inducing a significant increase (P ≤ 0.05) in cell proliferation of bone marrow cells. There is no increase in chromosomal aberrations following silymarin treatments. Results clearly showed that it significantly (P ≤ 0.05) decreased the MPE. Likewise, it was found to be a negative inducer of SCEs. It decreased in total abnormal metaphase, SCEs, MPE, and aberrant diakinesis.
CONCLUSION: The results demonstrated that silymarin has a strong anticlastogenic activity upon mice genome in somatic and germ cells, indicating its safe use as a medicinal substance. Furthermore, it is not only safe but also has protective effect from clastogens.

Matched MeSH terms: Chromosome Aberrations/drug effects

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