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Genetic study of 12 X-STRs in Malay population living in and around Kuala Lumpur using Investigator Argus X-12 kit

Samejima M, Nakamura Y, Nambiar P, Minaguchi K

Int J Legal Med, 2012 Jul;126(4):677-83.
PMID: 22584910 DOI: 10.1007/s00414-012-0705-7

We investigated 12 X-chromosomal short tandem repeat (STR) polymorphisms in 283 unrelated Malay individuals (160 males and 123 females) living in and around Kuala Lumpur using the Investigator Argus X-12 kit. Heterozygosity among the present 12 X-STRs showed a distribution of from 55.3 to 93.5 %. The diversity values of the haplotypes constructed using four closely linked groups were all higher than 0.9865. A comparison of allelic frequency in each system and haplotype variation indicated that the nature of these X-STRs in the Malay population differed from that in East Asian, European, or African populations. Several microvariant alleles found in the Malay population were characterized and compared with known sequence data. The present data may be helpful in forensic casework such as personal identification and kinship testing in the Malay population in Malaysia.

Matched MeSH terms: Chromosomes, Human, X*
Fulltext The triumvirate of NF-κB, inflammation and cytokine storm in COVID-19

Attiq A, Yao LJ, Afzal S, Khan MA

Int Immunopharmacol, 2021 Dec;101(Pt B):108255.
PMID: 34688149 DOI: 10.1016/j.intimp.2021.108255

The coronavirus disease (COVID-19) has once again reminded us of the significance of host immune response and consequential havocs of the immune dysregulation. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) inflicts severe complications to the infected host, including cough, dyspnoea, fever, septic shock, acute respiratory distress syndrome (ARDs), and multiple organ failure. These manifestations are the consequence of the dysregulated immune system, which gives rise to excessive and unattended production of pro-inflammatory mediators. Elevated circulatory cytokine and chemokine levels are accompanied by spontaneous haemorrhage, thrombocytopenia and systemic inflammation, which are the cardinal features of life-threatening cytokine storm syndrome in advanced COVID-19 diseases. Coronavirus hijacked NF-kappa B (NF-κB) is responsible for upregulating the expressions of inflammatory cytokine, chemokine, alarmins and inducible enzymes, which paves the pathway for cytokine storm. Given the scenario, the systemic approach of simultaneous inhibition of NF-κB offers an attractive therapeutic intervention. Targeted therapies with proteasome inhibitor (VL-01, bortezomib, carfilzomib and ixazomib), bruton tyrosine kinase inhibitor (acalabrutinib), nucleotide analogue (remdesivir), TNF-α monoclonal antibodies (infliximab and adalimumab), N-acetylcysteine and corticosteroids (dexamethasone), focusing the NF-κB inhibition have demonstrated effectiveness in terms of the significant decrease in morbidity and mortality in severe COVID-19 patients. Hence, this review highlights the activation, signal transduction and cross-talk of NF-κB with regard to cytokine storm in COVID-19. Moreover, the development of therapeutic strategies based on NF-κB inhibition are also discussed herein.

Matched MeSH terms: Chromosomes, Human, X/immunology
Fulltext Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

Machiela MJ, Zhou W, Karlins E, Sampson JN, Freedman ND, Yang Q, et al.

Nat Commun, 2016 06 13;7:11843.
PMID: 27291797 DOI: 10.1038/ncomms11843

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.

Matched MeSH terms: Chromosomes, Human, X/genetics*
Population data and genetic characteristics of 12 X-STR loci using the Investigator® Argus X-12 Quality Sensor kit for the Kedayan population of Borneo in Malaysia

Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Aziz MY, et al.

Int J Legal Med, 2021 Jul;135(4):1433-1435.
PMID: 33782746 DOI: 10.1007/s00414-021-02577-0

DNA profiling of X-chromosomal short tandem repeats (X-STR) has exceptional value in criminal investigations, especially for complex kinship and incest cases. In this study, Investigator® Argus X-12 Quality Sensor (QS) kits were successfully used to characterize 12 X-STR loci in 199 unrelated healthy Kedayan individuals living in Sabah and Sarawak, Malaysia. The LG1 haplogroup (DXS8378 - DXS10135 - DXS10148) has the largest HD (0.9799) as compared with all other closely linked haplotype groups examined (LG2; DXS7132-DXS10074-DXS10079, LG3; DXS10103-DXS10101-HPRTB and LG4; DXS10134-DXS7423-DXS10146). Data from statistical analysis showed that high combined of PDM, PDF, MEC_Krüger, MEC_Kishida, MEC_Desmarais, and MEC_Desmarais_duo values (0.999999994405922, 0.99999999999999, 0.999990463834938, 0.999999975914808, 0.999999975985006, and 0.999996491927194, respectively) in the Kedayan. In a two-dimensional scaling (MDS) plot and dendrogram constructed using allele frequencies at the 12 X-STR loci, Kedayan appear to be most closely related to their other Austronesian populations including the Malays and Filipinos as compared with other reference population groups. Findings from the present study thus demonstrate high genetic variability across the 12 tested X-STR loci and can be used for population studies and forensic applications.

Matched MeSH terms: Chromosomes, Human, X*
Fulltext A rare case of ambiguous genitalia

Ng SF, Boo NY, Wu LL, Shuib S

Singapore Med J, 2007 Sep;48(9):858-61.
PMID: 17728969

Genes on the Y chromosome are essential for normal sex determination and sex differentiation of male genitalia. However, genes on the X chromosome and other autosomes have been shown to be anti-testes and have a detrimental effect on this process. Addition of X chromosomes to the 46,XY karyotype results in seminiferous tubules dysgenesis, hypogonadism and malformed genitalia. We report a term male newborn with 49,XXXXY syndrome presenting with ambiguous genitalia, multiple extra-gonadal anomalies, facial dysmorphism, and radioulnar synostosis.

Matched MeSH terms: Chromosomes, Human, X/genetics*
A mother with variant Turner syndrome and two daughters with trisomy X: a case report

Ramachandram S, Keng WT, Ariffin R, Ganesan V

J Genet, 2013;92(2):313-6.
PMID: 23970090
Matched MeSH terms: Chromosomes, Human, X/genetics
Fulltext X-chromosome association study reveals genetic susceptibility loci of nasopharyngeal carcinoma

Zuo XY, Feng QS, Sun J, Wei PP, Chin YM, Guo YM, et al.

Biol Sex Differ, 2019 03 25;10(1):13.
PMID: 30909962 DOI: 10.1186/s13293-019-0227-9

BACKGROUND: The male predominance in the incidence of nasopharyngeal carcinoma (NPC) suggests the contribution of the X chromosome to the susceptibility of NPC. However, no X-linked susceptibility loci have been examined by genome-wide association studies (GWASs) for NPC by far.
METHODS: To understand the contribution of the X chromosome in NPC susceptibility, we conducted an X chromosome-wide association analysis on 1615 NPC patients and 1025 healthy controls of Guangdong Chinese, followed by two validation analyses in Taiwan Chinese (n = 562) and Malaysian Chinese (n = 716).
RESULTS: Firstly, the proportion of variance of X-linked loci over phenotypic variance was estimated in the discovery samples, which revealed that the phenotypic variance explained by X chromosome polymorphisms was estimated to be 12.63% (non-dosage compensation model) in males, as compared with 0.0001% in females. This suggested that the contribution of X chromosome to the genetic variance of NPC should not be neglected. Secondly, association analysis revealed that rs5927056 in DMD gene achieved X chromosome-wide association significance in the discovery sample (OR = 0.81, 95% CI 0.73-0.89, P = 1.49 × 10-5). Combined analysis revealed rs5927056 for DMD gene with suggestive significance (P = 9.44 × 10-5). Moreover, the female-specific association of rs5933886 in ARHGAP6 gene (OR = 0.62, 95%CI: 0.47-0.81, P = 4.37 × 10-4) was successfully replicated in Taiwan Chinese (P = 1.64 × 10-2). rs5933886 also showed nominally significant gender × SNP interaction in both Guangdong (P = 6.25 × 10-4) and Taiwan datasets (P = 2.99 × 10-2).
CONCLUSION: Our finding reveals new susceptibility loci at the X chromosome conferring risk of NPC and supports the value of including the X chromosome in large-scale association studies.

Matched MeSH terms: Chromosomes, Human, X*
Amelogenesis imperfecta: enamel ultra structure and molecular studies

Gopinath VK, Al-Salihi KA, Yean CY, Ann MC, Ravichandran M

J Clin Pediatr Dent, 2004;28(4):319-22.
PMID: 15366620

Amelogenesis imperfecta (AI) is a hereditary disorder resulting in generalized defects in the enamel. The case reported here is of a seven-year-old male child with yellow color of all his teeth. Two of his primary molars were extracted due to dental abscess with advanced root resorption. Histologically hypoplastic enamel layer, positively birefringent, generalized pitting, roughness with irregular general cracked borders were observed. Scanning electron microscope, revealed extensive irregular, disorganized rough superficial enamel layer. The enamel was irregularly decussate with filamentous prisms accompanied by small rounded formations. The morphological and histological examination of the tooth revealed that this patient has the features of AI. For genetic study blood sample were collected from the patient and PCR analysis revealed that there is no mutation in exons 1-7 of AMELX gene on the X chromosome of the patient. Hence, it is probable that the AI of this patient is not X-linked. It is more likely to be an autosomal mutation.

Matched MeSH terms: Chromosomes, Human, X/genetics
Fulltext Identification of Potential Genes for Benign Prostatic Hyperplasia and Prostate Cancer Susceptibility in Four X-chromosome Regions with High Frequency of Microvariant Alleles

Albujja MH, Messaudi SA, Vasudevan R, Al Ghamdi S, Chong PP, Ghani KA, et al.

Asian Pac J Cancer Prev, 2020 08 01;21(8):2271-2280.
PMID: 32856855 DOI: 10.31557/APJCP.2020.21.8.2271

BACKGROUND: The X-chromosome has been suggested to play a role in prostate cancer (PrCa) since epidemiological studies have provided evidence for an X-linked mode of inheritance for PrCa based on the higher relative risk among men who report an affected brother(s) as compared to those reporting an affected father. The aim of this study was to examine the potential association between the forensic STR markers located at four regions Xp22.31, Xq11.2-12, Xq26.2, and Xq28 and the risk of BPH and PrCa to confirm the impact of ChrX in the PrCa incidence. This may be helpful in the incorporation of STRs genetic variation in the early detection of men population at risk of developing PrCa.
METHODS: DNA samples from 92 patients and 156 healthy controls collected from two medical centers in Riyadh, Saudi Arabia were analyzed for four regions located at X-chromosome using the Investigator® Argus X-12 QS Kit.
RESULTS: The results demonstrated that microvariant alleles of (DXS7132, DXS10146, HPRTB, DXS10134, and DXS10135) are overrepresented in the BPH group (p < 0.00001). Allele 28 of DXS10135 and allele 15 of DXS7423 could have a protective effect, OR 0.229 (95%CI, 0.066-0.79); and OR 0.439 (95%CI, 0.208-0.925). On the other hand, patients carrying allele 23 of DXS10079 and allele 26 of DXS10148 presented an increased risk to PrCa OR 4.714 (95%CI, 3.604-6.166).
CONCLUSION: The results are in concordance with the involvement of the X chromosome in PrCa and BPH development. STR allele studies may add further information from the definition of a genetic profile of PrCa resistance or susceptibility. As TBL1, AR, LDOC1, and RPL10 genes are located at regions Xp22.31, Xq11.2-12, Xq26.2, and Xq28, respectively, these genes could play an essential role in PrCa or BPH.

Matched MeSH terms: Chromosomes, Human, X/genetics*
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: Chromosomes, Human, X
Fulltext Significance of a clean-tip catheter closed suctioning system in a high-setting ventilated, super morbidly obese patient with profuse respiratory secretions

Mazlan MZ, Mohd Zaini RH, Hassan SK, Ali S, Che Omar S, Wan Hassan WMN

Respir Med Case Rep, 2017;21:129-131.
PMID: 28487824 DOI: 10.1016/j.rmcr.2017.04.014

INTRODUCTION: Closed suctioning is commonly used in the context of high-setting mechanical ventilation (MV), given its ability to prevent lung volume loss that otherwise accompanies open suctioning. However, closed suctioning systems (CSS) are not equivalent regarding components and capabilities, and thus this technique may be differentially effective to adequately clear patient secretions from an endotracheal tube (ETT), which is of paramount importance when the tube size makes the ETT particularly vulnerable to block by patient secretions.
CASE PRESENTATION: A 25-year-old super morbidly obese female (body mass index = 55 kg/meter2) presented with worsening shortness of breath. For MV, pairing of a 6 mm (mm) diameter ETT to accommodate the patient's vocal cord edema, with a CSS not designed to maintain a clean catheter tip, precipitated ETT blockage and respiratory acidosis. Replacement of these devices with a 6.5 mm ETT and a CSS designed to keep the catheter tip clean resolved the complications. After use of the different ETT and CSS for approximately one week, the patient was discharged to home.
DISCUSSION: The clean-tip catheter CSS enabled a more patent airway than its counterpart device that did not have this feature. Use of a clean-tip catheter CSS was an important care development for this patient, because this individual's super morbidly obese condition minimized tolerance for MV complications that would exacerbate her pre-existing tenuous respiratory health status.
CONCLUSION: Special attention should be given to the choices of ETT size and CSS to manage super morbidly obese patients who have a history of difficult airway access.

Matched MeSH terms: Chromosomes, Human, X
Characterization of genetic sequence variation of 58 STR loci in four major population groups

Novroski NMM, King JL, Churchill JD, Seah LH, Budowle B

Forensic Sci Int Genet, 2016 11;25:214-226.
PMID: 27697609 DOI: 10.1016/j.fsigen.2016.09.007

Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X-chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups. Seven hundred and forty six autosomal, 227 X-chromosome, and 324 Y-chromosome STR alleles were identified by sequence compared with 357 autosomal, 107 X-chromosome, and 189 Y-chromosome STR alleles that were identified by length. Within the observed sequence variation, 227 autosomal, 156 X-chromosome, and 112 Y-chromosome novel alleles were identified and described. One hundred and seventy six autosomal, 123 X-chromosome, and 93 Y-chromosome sequence variants resided within STR repeat regions, and 86 autosomal, 39 X-chromosome, and 20 Y-chromosome variants were located in STR flanking regions. Three markers, D18S51, DXS10135, and DYS385a-b had 1, 4, and 1 alleles, respectively, which contained both a novel repeat region variant and a flanking sequence variant in the same nucleotide sequence. There were 50 markers that demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. These population data illustrate the genetic variation that exists in the commonly used STR markers in the selected population samples and provide allele frequencies for statistical calculations related to STR profiling with MPS data.

Matched MeSH terms: Chromosomes, Human, X
Fulltext Advanced paternal age effect on trisomy X syndrome

Ahzad Hadi Ahmad, Rabiatul Basria S.M.N. Mydin, Nur Ain Nisrina Roan, Abdul Rahman Azhari, Narazah Mohd Yusoff

Malaysian Journal of Medicine and Health Sciences, 2018;14(201):213-215.
MyJurnal

Advanced parental age is a risk factor for chromosomal abnormalities in their offspring. Trisomy X or Triple X syn- drome has previously been reported with advanced maternal age. Here we report two (2) cases of Trisomy X with paternal age as risk factor. Generally, Trisomy X individuals show variable physical and psychological manifesta- tions. However, both cases reported here have advanced paternal age as a risk factor; 55 years old (46 years old at conception) for Case 1 with patient having right eye squint, beaked nose, Posterior Misalignment Type Ventricular Septal Defect (PMVSD) and small Patent Ductus Arteriosus (PDA) with failure to thrive and 49 years old (45 years old at conception) for Case 2 with speech delay and protruding tongue. In view of that, advanced paternal age could possibly contribute the accumulation of de novo mutations in germ line mosaicism.

Matched MeSH terms: Chromosomes, Human, X
Fulltext Turner syndrome in diverse populations

Kruszka P, Addissie YA, Tekendo-Ngongang C, Jones KL, Savage SK, Gupta N, et al.

Am J Med Genet A, 2020 Feb;182(2):303-313.
PMID: 31854143 DOI: 10.1002/ajmg.a.61461

Turner syndrome (TS) is a common multiple congenital anomaly syndrome resulting from complete or partial absence of the second X chromosome. In this study, we explore the phenotype of TS in diverse populations using clinical examination and facial analysis technology. Clinical data from 78 individuals and images from 108 individuals with TS from 19 different countries were analyzed. Individuals were grouped into categories of African descent (African), Asian, Latin American, Caucasian (European descent), and Middle Eastern. The most common phenotype features across all population groups were short stature (86%), cubitus valgus (76%), and low posterior hairline 70%. Two facial analysis technology experiments were conducted: TS versus general population and TS versus Noonan syndrome. Across all ethnicities, facial analysis was accurate in diagnosing TS from frontal facial images as measured by the area under the curve (AUC). An AUC of 0.903 (p < .001) was found for TS versus general population controls and 0.925 (p < .001) for TS versus individuals with Noonan syndrome. In summary, we present consistent clinical findings from global populations with TS and additionally demonstrate that facial analysis technology can accurately distinguish TS from the general population and Noonan syndrome.

Matched MeSH terms: Chromosomes, Human, X/genetics

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