Background: Molecular biology of thymomas is poorly understood. We sequenced the whole genome of one B3 thymoma and the matched normal DNA from blood sample of the same patient. Methods: Frozen primary tumor and blood were collected from a Caucasian 53 female with B3/stage IVA thymoma after surgery. DNA and RNA were extracted using All Prep kit (Qiagen). Array Comparative genomic hybridization (CGH) was performed on 180K array (Agilent) and Agilent platform. Transcriptome sequencing was performed using 72bp paired-end sequencing and 2 flow cell lanes of genome analyzer II (Illumina). Whole genome sequencing (WGS) was performed on tumor and normal DNA using Complete Genomic Inc platform. Results: In the WGS analysis, a total of 222.02 gigabases (Gb) of sequence were mapped (95.3% of genome called) for the tumor sample and 234.53 Gb (96.4% of genome called) for the matched normal control. Sequence reads were aligned to a human reference genome (NCBI Build 37) and a local de novo assembly was used to call and score variants. Both array CGH and copy number (CN) aberrations estimated from WGS showed CN imbalance patterns comparable with those previously described for B3 thymomas with CN gain of chromosomes 1q, 5, 7 and X and CN loss of 3p, 6, 11q42.2-qter and q13. We observed 3,096,049 single nucleotide variations (SNVs) in the tumor and 3,314,611 in the normal DNA. The transition/transversion ratio was 2.14 and 1.83 for germ line and somatic SNVs, respectively. Somatic SNVs were defined as those variations present in tumor but not normal matched DNA. We observed 5946 diploid somatic indels and 6530 SNVs, of which 43 and 83 were within exonic regions, respectively. 29 indels and 25 SNVs were not previously described as SNPs, nor in segmental duplication, or synonymous mutations. By comparison with the transcriptome sequencing data of the same tumor sample, we confirmed the expression of 6 mutated genes, while for 45 mutated genes there were not enough reads to confirm the calls. Conclusion: WGS and accompanying transcriptome sequencing offer an unprecedented view of the genome of a thymoma cancer patient sample. We are actively engaged in determining the potential functional significance of the genomic variants in the context of transcriptome sequencing and copy number variation to gather clues as to the underlying biology driving this relatively rare tumor type.
COMPLETE GENOME SEQUENCING OF A HUMAN B3 THYMOMA
PETRINI, IACOPO;
2011-01-01
Abstract
Background: Molecular biology of thymomas is poorly understood. We sequenced the whole genome of one B3 thymoma and the matched normal DNA from blood sample of the same patient. Methods: Frozen primary tumor and blood were collected from a Caucasian 53 female with B3/stage IVA thymoma after surgery. DNA and RNA were extracted using All Prep kit (Qiagen). Array Comparative genomic hybridization (CGH) was performed on 180K array (Agilent) and Agilent platform. Transcriptome sequencing was performed using 72bp paired-end sequencing and 2 flow cell lanes of genome analyzer II (Illumina). Whole genome sequencing (WGS) was performed on tumor and normal DNA using Complete Genomic Inc platform. Results: In the WGS analysis, a total of 222.02 gigabases (Gb) of sequence were mapped (95.3% of genome called) for the tumor sample and 234.53 Gb (96.4% of genome called) for the matched normal control. Sequence reads were aligned to a human reference genome (NCBI Build 37) and a local de novo assembly was used to call and score variants. Both array CGH and copy number (CN) aberrations estimated from WGS showed CN imbalance patterns comparable with those previously described for B3 thymomas with CN gain of chromosomes 1q, 5, 7 and X and CN loss of 3p, 6, 11q42.2-qter and q13. We observed 3,096,049 single nucleotide variations (SNVs) in the tumor and 3,314,611 in the normal DNA. The transition/transversion ratio was 2.14 and 1.83 for germ line and somatic SNVs, respectively. Somatic SNVs were defined as those variations present in tumor but not normal matched DNA. We observed 5946 diploid somatic indels and 6530 SNVs, of which 43 and 83 were within exonic regions, respectively. 29 indels and 25 SNVs were not previously described as SNPs, nor in segmental duplication, or synonymous mutations. By comparison with the transcriptome sequencing data of the same tumor sample, we confirmed the expression of 6 mutated genes, while for 45 mutated genes there were not enough reads to confirm the calls. Conclusion: WGS and accompanying transcriptome sequencing offer an unprecedented view of the genome of a thymoma cancer patient sample. We are actively engaged in determining the potential functional significance of the genomic variants in the context of transcriptome sequencing and copy number variation to gather clues as to the underlying biology driving this relatively rare tumor type.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
