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Biomedical subjects

R V Shaji

Publications and source records attributed to R V Shaji.

At least 19 recordsLinked to original sources
PubMed2006

Developing an algorithm of informative markers for evaluation of chimerism after allogeneic bone marrow transplantation.

Analysis of chimerism by polymerase chain reaction amplification of STR or VNTR has become a routine procedure for the evaluation of engraftment after allogeneic stem cell transplantation. Knowledge of the frequency of different STR or VNTR alleles in unrelated individuals in a population is useful for forensic work. In the context of HLA identical sibling bone marrow transplantation the informativeness of these markers needs to be evaluated. We evaluated five STRs (THO1, VWA, FES, ACTBP2, and F13A1) and 1 VNTR (APOB) for informativeness in stem cell transplants from HLA identical sibling donors. All four markers used individually allowed us to discriminate 20-56% of the patient donor pairs. Using a combination of all these markers along with a polymorphic marker in the beta-globin gene and the sex chromosome specific amelogenin marker, we were able to discriminate 99% of the patient donor pairs. We have established an algorithm for evaluating chimerism following HLA identical sibling donor transplants in the Indian population using molecular markers in 310 patients. Analysis of heterozygote frequencies in different populations is similar suggesting that this algorithm can be used universally for transplant centers to evaluate chimerism following allogeneic bone marrow transplantation.

Algorithms↗
PubMed2005

Six novel mutations including triple heterozygosity for Phe31Ser, 514delT and 516T-->G factor X gene mutations are responsible for congenital factor X deficiency in patients of Nepali and Indian origin.

Factor X (FX) deficiency is a rare (1 : 100000) autosomal recessive disorder caused by heterogeneous mutations in FX gene. We have studied the molecular basis this disease in six Indian and one Nepali patients. Diagnosis was confirmed by measuring the FX coagulant activity (FX: C) using a PT based assay. Six of them had a FX: C of < 1% and one patient had 24% coagulant activity. Mutations were identified in all the seven patients. These included eight (88.8%) missense and one frame-shift (11.2%) mutations of which six were novel. Three of the novel mutations, a Phe31Ser affecting 'Gla' domain and 514delT and 516T-->G mutations affecting Cys132 in 'connecting region' were identified in a triple compound heterozygous state in a Nepali patient presenting with a severe phenotype. Two other novel mutations, Gly133Arg, may affect the disulphide bridge between Cys132-Cys302 in the connecting region while Gly223Arg may perturb the catalytic triad (His236, Asp282 and Ser379). The other novel mutation, Ser354Arg, involves the replacement of a small-buried residue by a large basic aminoacid and is likely to have steric or electrostatic effects in the pocket involving Lys351-Arg347-Lys414 that contributes to the core epitope of FXa for binding to FVa. Three previously reported mutations, Thr318Met; Gly323Ser; Gly366Ser were also identified. This is the first report of the molecular basis of FX deficiency in patients from the Indian subcontinent.

Arginine↗
PubMed2005

Fludarabine-based conditioning for allogeneic stem cell transplantation for multiply transfused patients with Fanconi's anemia.

A fludarabine-based protocol (fludarabine (25 mg/m(2)/day x 6 days), cyclophosphamide (10 mg/kg/day x 2 days) and ATG (ATGAM 10 mg/kg/day x 4 days)) was used in four multiply transfused Fanconi's anemia (FA) patients aged 5-15 years to reduce rejection during allogeneic bone marrow transplantation (BMT). Graft-versus-host disease (GVHD) prophylaxis consisted of cyclosporine and mini methotrexate. The graft source was G-CSF-stimulated bone marrow or peripheral blood stem cells (PBSC) in two patients each. All patients engrafted with median time to ANC>500/mm(3) being 14 days (range: 12-17) and unsupported platelet count >20 ,000/mm(3) being 13 days (range: 11-18). One patient had secondary graft rejection on day 56 and expired on day 69 due to fungal pneumonia. One patient who developed acute myeloid leukemia on day 56 underwent successful induction with cytosine and daunorubicin followed by peripheral blood stem cell (PBSC) rescue on day 70 and is presently in remission with complete donor chimerism and grade I GVHD. At a median follow-up of 13 months (range: 4-21), three patients (75%) are well with complete donor chimerism. Addition of fludarabine to the conditioning regimen for BMT in FA can provide additional immunosuppression for engraftment without increasing toxicity.

Adolescent↗
PubMed2005

Investigation of persistent hypochromic microcytosis unmasks hemoglobin Evanston [alpha 14 (A12) Try--> Arg] in a patient of cyclic thrombocytopenia preceding Takayasu's disease.

We report an unusual north Indian patient with Hemoglobin Evanston [alpha 14 (A12) Try --> Arg] who had acquired cyclic thrombocytopenia (10-1230 x 10(9)/l periodic oscillation of four week duration) which recovered without any specific therapy. She later developed Takayasu's disease and underwent three corrective stents. She is presently in clinical remission and is on regular follow up. To the best of our knowledge our patient is the first report of Hb Evanston from the indigenous population of India and highlights the need to look for point mutations in the alpha globin gene, which may interact with thalassemia or other hemoglobinopathies, in atypical cases. The association of these three disorders in our patient is possibly unrelated though an immune basis for the cyclic thrombocytopenia and Takayasu's disease is likely as seen in this report.

Adult↗
PubMed2005

Identification of factor VIII gene mutations in 101 patients with haemophilia A: mutation analysis by inversion screening and multiplex PCR and CSGE and molecular modelling of 10 novel missense substitutions.

Haemophilia A (HA) is an X-linked bleeding disorder caused by diverse mutations in the human coagulation factor VIII (FVIII) gene. We have analysed DNA from 109 unrelated Indian patients with HA for their FVIII gene defects. Among these patients 89 (82%) had severe (FVIII:C <1%) HA, 11 (10%) had moderate (FVIII:C 1-5%) HA and nine (8%) had mild (FVIII:C 5-30%) HA. These patients were first screened for the common intron 22 and intron 1 inversions. Inversion negative samples were screened for point mutations by a multiplex PCR and conformation sensitive gel electrophoresis strategy. Mutations were identified in 101 of the 109 patients. These included two (2%) intron 1 and 51 (51%) intron 22 inversions, four (4%) gross deletions and 44 (43%) point mutations. Twenty-nine novel causative mutations, including 11 missense, seven frameshift, five nonsense mutations, three splice site defects and three gross deletions were detected. Ten of the novel missense mutations were studied by molecular modelling. Two different (Thr2253Pro and Pro1392fs) mutations were seen in four unrelated families and FVIII gene haplotyping suggested a common founder effect. Seven of these 109 patients had inhibitors. Among them, four had intron 22 inversions, one had a novel gross deletion (delexon 2-9) and one a nonsense mutation (Trp1535Stop). In one of these patients, no mutation could be identified in the FVIII gene. A Thr2253Pro novel mutation and an intron 22 inversion were identified in two female haemophiliacs. The data from this study suggests that the spectrum of gene defects in Indian patients with HA is as heterogeneous as reported in other populations.

Amino Acid Substitution↗
PubMed2005

Molecular genetics of hereditary prothrombin deficiency in Indian patients: identification of a novel Ala362 --> Thr (Prothrombin Vellore 1) mutation.

Prothrombin deficiency is a rare (1:200 000) autosomal recessive disorder caused by diverse mutations in prothrombin gene. We have studied the molecular basis of this disorder in four unrelated Indian patients. The diagnosis was based on prolonged prothrombin (PT) and activated partial thromboplastin times and low factor II coagulant activity (FII: C) measured using a PT based assay. FII: C levels ranged between 4.7% and 17.5%. Mutations were identified in all the four patients. Five different causative mutations including four (80%) missense and an in-frame deletion (20%) were identified. One of them was a novel, Ala362 --> Thr amino acid change affecting 'B' chain of -thrombin. This mutation was present in a compound heterozygous state with a previously reported Arg-1 --> Gln missense change affecting pro-peptide cleavage site. Ala362 --> Thr occurred at a codon, evolutionarily conserved in all the 24 different prothrombins or its related serine proteases studied. Molecular modeling of this mutation was found to cause a conformational change around the region involving a catalytic triad residue His363 and a cysteine residue at codon 364. The FII: C level in this patient was 17.5%. Three other previously reported mutations were also detected in the homozygous state: Arg271 --> Cys in Kringle-2 region, a Glu309 --> Lys in "A" chain of -thrombin and an in-frame deletion of 3 bp (AAG) leading to Del Lys301/302 in "A" chain of -thrombin. This is the first report of the molecular basis of prothrombin deficiency in Indian patients and we suggest the eponym 'Prothrombin Vellore 1' for Ala362 --> Thr mutation.

Adult↗
PubMed2005

Cytochrome P4501A1 and glutathione S transferase gene polymorphisms in patients with aplastic anemia in India.

The etiology of acquired aplastic anemia (AA) in most patients remains unclear. It is believed that patients with a reduced ability to detoxify environmental toxins are at increased risk of developing AA. Cytochrome P450 (CYP450) and glutathione S transferase (GST) are the major phase I and phase II xenobiotic-metabolizing enzymes. We analyzed the impact of the polymorphisms in CYP4501A1 and GSTM1 and GSTT1 genes on the susceptibility and disease severity in 200 patients with AA and compared the frequency with the normal population. There was a significantly increased frequency of the CYP1A1m4 allele in AA patients compared with normal controls (odds ratio = 3.01; 95% confidence interval 1.76-5.17; p = 0.00001). None of the other CYP1A1 genotypes or the GST genotypes were significantly different between AA patients and controls. Altered metabolism of benzo(a)pyrene due to the polymorphism in the CYP1A1 gene might be an etiologic factor in the increased incidence of AA in these patients. The CYP1A1m4 allele may play a role in determining the risk of AA in India.

Adolescent↗
PubMed2004

HPV DNA in plasma of patients with cervical carcinoma.

BACKGROUND: HPV DNA has been detected in metastatic tumour and HPV plasma viraemia may indicate a poor prognosis and a high risk for metastasis. OBJECTIVE: Detection of HPV DNA in plasma of patients with cervical carcinoma. STUDY DESIGN: A cross-sectional study was done, wherein cervical biopsies and plasma samples were collected from 58 women with invasive cervical carcinoma, 10 women with cervical intraepithelial neoplasia (CIN) and 30 control women in the same age range. Polymerase chain reaction (PCR) was employed to detect the presence of HPV DNA. Samples positive for HPV DNA were typed by restriction fragment length polymorphism (RFLP). To confirm that the HPV sequence in plasma was identical to that in tissue, sequencing was done on all the paired plasma and tissue samples. RESULTS: All the 30 paired cervical tissue and plasma samples from the controls were negative for HPV DNA. HPV DNA was detectable in cervical tissues of 55 (94.8%) of 58 patients with invasive cervical carcinoma and in all 10 patients (100%) with CIN and in eight (11.8%) of the total 68 plasma samples from patients. All eight plasma samples were from women with invasive cervical carcinoma with three each in stages IIIB and IV and one each in stages IIB and IB, respectively. Of the eight positive samples, seven were typed as HPV-16 and 1 as HPV-58. HPV types detected in cervical tissue and plasma pairs from these eight patients correlated as revealed by RFLP and sequencing. A patient with stage IB cancer had detectable HPV DNA in the external iliac lymph node, removed at Wertheims hysterectomy, which was histopathologically free of tumour. The HPV type in the node, was the same as that present in the paired tissue and plasma sample. CONCLUSIONS: HPV DNA is detectable in the plasma of patients with advanced cervical cancer.

Adult↗
PubMed2004

HCV genotype 4--an emerging threat as a cause of chronic liver disease in Indian (south) patients.

BACKGROUND: Hepatitis C virus (HCV) genotyping is relevant for the delivery of effective antiviral therapy. HCV genotypes are geographically restricted with genotype 4, which is resistant to therapy, traditionally considered to be confined to the Middle East and Africa. We report here on the occurrence of HCV genotype 4 in Indian (South) patients. OBJECTIVES: 1) To highlight the occurrence of HCV genotype 4 in the patient population attending a tertiary care hospital in south India. 2) To ascertain the difference in HCV viral loads and alanine aminotransferase (ALT) values between patients infected with HCV genotype 4 and those infected with the other two most commonly detected genotypes in this patient population viz., HCV genotypes 1 and 3. 3) To assess the genetic relatedness of the Indian strains to Genbank sequences, which we report for the first time. STUDY DESIGN: The study group consisted of 125 HCV infected, untreated patients who had been genotyped using type specific primers. Eight of the nine samples classified as HCV genotype 4 by this technique were subjected to nucleotide sequencing. Viral load estimations were carried out. Information on possible risk factors and ALT values were obtained from hospital records. Statistical analyses were carried out to compare viral loads and ALT values across genotypes. A phylogenetic tree was constructed and the genetic relatedness of the strains was assessed through sequence analysis. RESULTS: HCV genotype 4 was detected in nine of 125 (7.2%) patients. Eight of the nine were subjected to nucleotide sequencing and all strains were confirmed as HCV genotype 4. Six of the eight strains were closely related, with two strains being phylogenetically diverse. CONCLUSIONS: HCV genotype 4 is detected in a significant minority of HCV infected patients in India. This finding should be considered in designing strategies prior to initiation of therapy in Indian patients infected with HCV.

Adult↗
PubMed2004

E2 sequence variations of HPV 16 among patients with cervical neoplasia seen in the Indian subcontinent.

OBJECTIVES: Specific nucleotide variations in the E2 DNA sequence were looked for in samples with an intact human papillomavirus (HPV) 16 episomal E2 DNA. METHODS: Ninety-two women, 76 with invasive cervical carcinoma and 16 with cervical intraepithelial neoplasia (CIN) were recruited. HPV DNA typing was performed by polymerase chain reaction (PCR) based restriction fragment length polymorphism (RFLP). Intact episomal E2 DNA of HPV 16 was detected by PCR. Important nucleotide variations in samples with amplifiable E2 DNA were detected by RFLP. Nucleotide sequencing was performed on representative samples to confirm RFLP findings. RESULTS: A total of 89 (96.7%) women were positive for HPV DNA. Of these, 56 (63%) were positive for HPV 16, and of these, 38 (68%) were positive for intact episomal HPV 16 E2 DNA while 18 (32%) were negative. Samples with intact episomal HPV 16 E2 DNA sequences were grouped into four different digestion profiles I to IV based on RFLP patterns. Digestion patterns revealed absence of any sequence variations in samples with digestion profile I and presence of a 2983 A-G variation in those with profile II. Samples with digestion profiles III and IV revealed three variations in the hinge region (3516 C-A, 3538 A-C, 3566 T-G) and two in the DNA binding domain (3684 C-A, 3694 T-A) of the E2 sequence. Sequencing performed on representative samples confirmed RFLP findings. CONCLUSIONS: PCR-RFLP helped in the identification of important HPV 16 E2 sequence variations, circumventing the need for sequencing. The presence of the nucleotide variations in positions that could alter the biological and immunological functions of the E2 protein combined with its increased occurrence in this study bring out the importance of these variations.

Base Sequence↗
PubMed2004

Treatment of children with newly diagnosed acute promyelocytic leukemia with arsenic trioxide: a single center experience.

A total of 11 children (five males and six females) with hypergranular type of acute promyelocytic leukemia (APML) were treated with intravenous arsenic trioxide (As(2)O(3)) between December 1998 and October 2003. Eight cycles of As(2)O(3) (0.15 mg/kg/day) were administered (induction, consolidation and six cycles of maintenance) over a period of 12 months. The median WBC count at diagnosis was 3400/mm(3) (range: 800-9800). In all, 10 patients (91%) achieved hematological remission at a mean duration of 48 days (range: 41-60) with all 10 patients achieving molecular remission at a median duration of 81 days (range: 64-109). Toxicity was minimal with leukocytosis in six patients, ichthyosis and hyperpigmentation of skin in five and mild peripheral neuropathy in one patient. One patient who relapsed 6 months after completing therapy achieved a second hematological and molecular remission with As(2)O(3). With a median follow-up of 30 months (range: 4-62), the overall (OS) survival is 91% with a relapse-free survival (RFS) of 81%. As(2)O(3) achieves hematological and molecular remission in majority of newly diagnosed children with APML with minimal toxicity, but long-term follow-up is required to evaluate late effects of As(2)O(3) and study the minimum dose and duration required for a sustained remission.

Adolescent↗
PubMed2004

Informativeness of linkage analysis for genetic diagnosis of haemophilia A in India.

The objective of this study was to assess the frequency of factor VIII (FVIII) gene intron 1 and intron 22 inversions and the informativeness of polymorphic markers for the genetic diagnosis of patients with haemophilia A (HA). Fifty unrelated patients with HA were first assessed for the intron 1 and intron 22 inversion mutations. Inversion-negative families were then screened for the bi-allelic intragenic markers--intron 7 G-->A polymorphism, HindIII site in intron 19 and XbaI site in intron 22 and the multiallelic dinucleotide CA repeat alleles in introns 13 and 22. The extragenic, multiallelic VNTR DXS52 (st14) was also analysed. Intron 22 inversion mutation was found in 38% (n = 19) of all patients and 46% of those with severe HA. Intron 1 inversion was found in one (2%) patient. Of the 30 inversion-negative families, XbaI site polymorphism was the single most informative marker (70%, n = 21/30) followed by HindIII (60%, n = 18/30), intron 13 CA repeats (56.66%, n = 17/30), intron 22 CA repeats (50%, n = 15/30), DXS52 VNTR (23.33%, n = 7/30) and intron 7 G-->A polymorphism (6.66%, n = 2/30). The combined use of these markers was informative in 92% (n = 46/50) of HA families. Based on the informativeness of these markers a comprehensive algorithm has been proposed for genetic diagnosis of HA in India.

Chromosome Inversion↗