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Completed Projects

  Parental origin of extra chromosome 21 in Down syndrome children and its association with congenital heart disease

Principal Investigator : Dr. V. Babu Rao
Duration : 2007-2010 (3 years)
Funding agency: ICMR (Intra mural)

 


  Summary :

A high frequency of maternal Contribution of extra chromosome 21 detected in DS. The maternal meiotic I non-disjunction was more. A high frequency of MTHFR polymorphism was detected in mothers of DS children with Congenital heart disease. A high frequency of DS children born to young parents .

 


  Susceptibility to BCR-ABL gene in in vitro and ex-vivo studies.

  1. PI: Dr. K. Ghosh
  2. Co-PI: Dr. V. Babu Rao
  3. Duration : 2010-2013
  4. Funding agency : ICMR (Extra mural)
 


  Summary

The study was carried out 220 CML patients and 171 patients participated in the follow up study. Seventy eight (78) showed imatinib resistance or suboptimal response. Among 78 CML patients exhibiting clinical resistance to imatinib, 41% (32/78) of patients had mutations in the ABL KD of the BCR/ABL gene. The frequency of mutations was found to be more in the P-loop, accounting to 44% (14/32) of the total mutations. The most common and the highly resistant mutation found in the P-loop was Y253H/F with a frequency of 22% (7/32) and the PPHv2 damaging score of 1, followed by G25oE, 13% (4/32) and with the PPHv2 damaging score of 0.993. Most of the patients (25/32) harboring mutations were in the chronic phase of the disease. Only 4(5.1%) patients showed the presence of mutations in the regulatory domain of the BCR/ABL gene (SH2-SH3). Patients with mutations in the P-loop had a particularly poor prognosis. More patients with haematologic resistance had mutations compared to patients with cytogenetic resistance. Thus a poor hematologic response can be considered as a good indicator of the presence of mutations in the BCR/ABL gene. Lack of major cytogenetic response by 12 months was also associated with higher likelihood detecting a mutation. Forty two (42) CML patients with IM resistance and not harboring mutations in the BCR/ABL gene were considered for the study of pharmacogenetic variation and drug metabolizing enzymes. Our study showed that the SNP, CYP3A4*1B not associated with the drug resistance. However significant difference was observed for CYP3A5*1/*3 SNP between responders and non-responders, indicating a possible role of the expressor phenotype CYP3A5*1/*3 I imatinib metabolization and hence imatinib resistance in Indian patients with CML. The study also demonstrated that the frequency of AA genotype for M408 SNP of hOCT1 gene was in resistant group. Thus AA genotype for M408 SNP can be considered as a good indicator of poor imatinib response. In conclusion, close monitoring at regular intervals and proper analysis of different mechanisms of disease resistance would facilitate early detection of resistance and thus aid in selection of the most appropriate therapy.

 


  Molecular screening of Fanconi anemia complementation groups in Indian population.

  1. PI : Dr. V. Babu Rao
  2. Co-PI : Dr. K. Ghosh
  3. Duration : 2010-2013
  4. Funding agency : ICMR extramural
 


  Summary :

The study was carried out in 535 patients suspected with Fanconi anemia (FA). The FA was diagnosed by chromosomal breakage investigation. Sixty six (66) patients found to have high frequency of chromosomal breakage and diagnosed as FA. All the patients were confirmed with FANCD2 monoubiquitination by western blotting. Sixty four patients had up stream gene defects in FA pathway i.e FA-A,C,G etc genes. Only two cases showed FAND2 monoubiquitination suggesting down stream gene defects in FA pathway. Complementation analysis of FA genes carried out in 64 FA patients. FA complementation group A was detected in 46 (71.88%) patients. The FA-C and FA-G complementation groups were detected in 10 (15.63%) and 8 (12.4%) patients respectively. Mutation analysis of FANCA gene revealed large deletions by MLPA in 9 FA, novel gene mutations in 6 FA patients. The polymorphisms relevant to the disease found in 12 cases. However the reported polymorphisms also detected in 15 cases but need to be correlated with the disease. The novel mutations in FANCC was detected in 2 cases. The parents were counseled according to the gene mutations. The complete molecular analysis is in the process. This is the first study from in Indian population.

 


  Clinical significance of deletions of BCR/ABL gene (9q34) and microRNA expression in chronic myeloid leukemia (CML) patients.

  1. PI: Dr. V. Babu Rao
  2. Co-PI: Dr.K.Ghosh
  3. Duration : 2010-2013
  4. Funding agency : CSIR.
 


  Summary :

A total of 150 CML patients were analysed to identify 9q deletion. Fluorescent in-situ hybridization (FISH) was performed using BCR/ABL dual color, dual fusion probe to study the signal pattern and 34 (23%) patients found to had 9q deletion (ABL).
BAC probes for miR-199b and miR-219-2 (RP11-339B21 and RP11-395P17) to study the miRNA deletions. The deletions were not detected using BAC probes for miRNAs in 9q deleted patients.
The expression level of miRNA was analysed by real-time polymerase chain reaction (RT-PCR). The expression analysis showed down-regulation of miR-199b and miR-219-2 in the 9q deleted patients (34 CML) as compared to a pool of patients without deletion. However, miR-199b (9q34.11) was significantly (p=0.001) down-regulated compared to miR-219-2.
The follow-up study showed that the miR-199b was found to be strongly associated with imatinib resistance, as 44.11% patients showed resistance to imatinib therapy.
Hence, the deletion on 9q34.1 region (ABL) plays an important role in disease pathogenesis. Eventually, miRNAs can provide new therapeutic strategies and can be used as a prognostic indicator.

 


  Cytogenetic and Molecular study of Myelodysplastic syndrome

  1. PI: Dr. V. Babu Rao
  2. Co-Investigator : Dr. K. Ghosh
  3. Duration : 2013-ongoing
  4. Funding Agency: Department of Atomic Energy (DAE), BRNS

Expected outcome
The study is expected to identify genetic including chromosomal aberrations and molecular mutations (ASXL,TET2,TP53 etc) and non genetic factors such as occupational exposure and habits in the development of MDS. The study also designed a QMPSF assay and expected to identify copy number changes in 25 genes .

 


  Study of single nucleotide polymorphisms (SNPs) of multiple candidate genes (ABCB1, ABCG2, CYP3A4, CYP3a5,SLCO1B3, AGP1, SLC22A1) in Imatinib resistance chronic myeloid leukemia".

  1. PI : Dr. V. Babu Rao
  2. Co-PI: Dr.Chandrakala S
  3. Duration : 2014-ongoing
  4. Funding Agency: CSIR

Expected Outcome
SNP study of Multiple Candidate gene will help in pharmacogenomics of drug resistance CML patients and establish genetic markers for patients not responding to Imatinib therapy.

 


  Molecular Study of telomerase RNA component (TERC) gene, telomerase reverse transcriptase (TERT) and dyskeratosis congenita (DKC1) gene in idiopathic aplastic anemia

  1. PI: Dr. V. Babu Rao
  2. Co-PI: Dr. Chandrakala S
  3. Duration : 2015-ongoing
  4. Funding Agency : ICMR

Expected Outcome
Variations in telomerase activity will be detected in patients with aplastic anemia. The genetic basis of telomerase activity and telomere shortening will be assessed by the study of telomerase gene mutations. The study expected to find the correlation of telomerase activity and disease condition after ATG therapy.

 


  Services

  1. Cytogenetic evaluation of hematological malignancies (CML,AML,MDS, ALL, multiple myeloma).
  2. Karyotyping of patients suspected with genetic diseases.
  3. Fluorescence in situ hybridization (FISH) investigation in hematological malignancies.
  4. FISH study in selected cases of patients suspected with genetic diseases. (X and Y chromosome aberrations, patients with numerical chromosomal abnormalities 21, 13 , 18, 22 etc)
  5. Chromosomal breakage investigation in Fanconi anemia
  6. Sister chromatid exchanges study in Bloom syndrome.
  7. Chromosomal breakage and molecular mutation detection in Ataxia Telangiectasia.
  8. FANCD2 western blotting in Fanconi anemia.
  9. Molecular mutation detection of FANCA,C,G genes and prenatal diagnosis
  10. Mutation analysis in Dyskeratosis congenita
 


  Awards & Fellowships

  1. Junior Research Fellow and GATE Fellowship, University Grants Commission, 1990.
  2. BOYSCAST Fellowship by Department of Science & Technology (DST) 2001. Worked as BOYSCAST fellow at Department of Genetics, University of Bari, Italy, April to September 2001.
  3. 3. Young Bio-Medical Scientist ward by Indian Council of Medical Research, 2008. Worked at Dana Farber Cancer Institute, Harvard Medical School, Boston, USA, April to September 2008.
 


  International Collaborations

  1. Indo -Bulgarian project on "Molecular Genetics, Immunological and Functional study of the multidrug resistance in patients with leukemias" by DST, 2006
  2. Indo-Japan (JSPS) project on "Collaborative effort to understanding and characterization of novel molecular changes in Fanconi anemia (FA)" by DST, 2015.