Cancer Genome and Exome Sequencing in 2011

As a follow-up to my previous post, Disease-causing Mutations Discovered by NGS in 2011, I’ve attempted to compile cancer genome and exome sequencing studies published last year. For this compilation, I’ve emphasized publications in which whole-genome or exome sequencing was employed to multiple tumors or cancer cell lines, with the goal of identifying significantly altered genes or pathways in malignant cells. Even with these restrictions, the list of papers in 2011 was rather extensive. Links are provided to Pubmed for the citations; when a “key finding” is a link, it points to previous Massgenomics posts on the study. I’ve broken the publications down into several categories:

Cancer whole-genome sequencing
Exome sequencing of leukemia
Exome sequencing of carcinoma
Exome sequencing of melanoma
Pancreatic, gastric, and prostate cancer exomes

Whole-genome sequencing (WGS) studies

Several whole-genome sequencing studies of cancer were published last year. The largest of these was a study from the Broad Institute, in which whole-genome sequencing or exome sequencing was applied to 38 multiple myeloma tumors.

Cancer Whole-genome Sequencing
Cancer Type	#Samples	Key Finding(s)	Publication
Myelodysplastic syndrome (MDS)	1 WGS 150 case extension	Recurrent mutations the U2AF1 splicing factor	Graubert et al. Nat. Genet.
HCV+ Hepatocellular carcinoma	1 case	Transcription-coupled DNA repair; several gene fusion events including BCORL1-ELF4	Wei et al. Nat. Genet.
Chronic lymphocytic leukemia	4 cases	Recurrent mutations in NOTCH1, XPO1, MYD88, and KLHL6	Puente et al. Nature
Colorectal adenocarcinoma	9 cases	Recurrent VTI1A-TCF7L2 fusions (3%)	Bass et al. Nat. Genet.
Prostate cancer	7 cases	Rearrangements disrupting CADM2, PTEN, or MAGI2	Berger et al. Nature
Multiple myeloma	22 WGS, 15 Exome, 1 both	Activating mutations in BRAF (4%)	Chapman et al. Nature
Therapy-related AML	1 case	Novel heterozygous 3-kilobase deletion affecting TP53 in germline DNA	Link et al. JAMA
Non-Hodgkin lymphoma	14 cases +113 RNA-seq	Frequent mutation of MLL2 (32%/89%) and MEF2B (11.4%/13.4%) in DLBCL/FL.	Morin et al. Nature

Exome sequencing of leukemia

Several types of leukemia were characterized by exome sequencing, including chronic lymphocytic leukemia (CLL), acute myeloid leukemia (AML), acute monocytic leukemia (M5 AML), and pediatric acute lymphocytic leukemia (ALL).

Exome Sequencing of Leukemia
Cancer Type	#Samples	Key Finding(s)	Publication
CLL	105 cases	Recurrent mutations of the splicing factor SF3B1	Quesada et al. Nat Genet 2011.
M5 AML	9 cases	Somatic mutations of DNMT3A	Yan et al. Nat Genet 2011.
AML (normal karyotype)	1 exome 553 case extension	Somatic mutations in BCOR	Grossmann et al. Blood 2011.
Pediatric ALL	2 cases	4-7 somatic protein-altering mutations per case	Lilljebjorn et al. Leukemia 2011.

Exome sequencing of carcinoma

Exome sequencing was also applied to many solid organ tumors, particularly carcinomas. The Cancer Genome Atlas research network published a landmark study of high-grade serous ovarian carcinoma, the first of several common cancers to be characterized by TCGA. A number of other TCGA efforts will likely see publication in 2012, including breast cancer, colorectal cancer, glioblastoma, and leukemia.

Exome Sequencing of Carcinoma
Cancer Type	#Samples	Key Finding(s)	Publication
Serous ovarian	316 cases	Recurrent mutations in TP53, NF1, BRCA1, BRCA2, RB1 and CDK12	TCGA, Nature 2011.
Head and neck squamous cell	74 cases	Mutations in TP53, CDKN2A, PIK3CA, HRAS, and squamous differentiation genes.	Stransky et al. Science.
Head and neck squamous cell	32 cases	Mutations in TP53, CDKN2A, PIK3CA, and HRAS, FBXW7 and NOTCH1. Tumor-suppressor role for NOTCH1.	Agrawal et al. Science 2011.
Renal carcinoma	7 cases	Frequent mutation of the SWI/SNF complex gene PBRM1	Varela et al. Nature 2011.

Exome sequencing of melanoma

Melanoma was another cancer type surveyed by multiple exome sequencing studies in 2011. Interestingly, two studies of melanoma cell lines revealed frequent mutations in mitogen activated protein (MAP) kinase kinase [kinase] genes MAP2K1, MAP2K2, MAP3K5, and MAP3K9.

Exome Sequencing of Melanoma
Cancer Type	#Samples	Key Finding(s)	Publication
Melanoma	14 cases	Frequent mutations in GRIN2A	Wei et al. Nat Genet. 2011.
Metastatic Melanoma	8 cell lines	Mutations in MAP3K5 and MAP3K9	Stark et al. Nat Genet. 2011
Melanoma	7 cell lines	Recurring somatic MAP2K1 and MAP2K2 mutations (8%)	Nikolaev et al. Nat Genet. 2011

Pancreatic, gastric, and prostate cancer

Finally, I have a category of “other cancers” with exomes published in 2011; these include pancreastic cysts and cell lines, gastric cancer tumors, and prostate cancer samples derived through mouse xenograft models.

Pancreatic, Gastric, and Prostate Cancer Exomes
Cancer Type	#Samples	Key Finding(s)	Publication
Pancreatic cancer	15 cell lines	Genomic instability caused by MLH1 haploinsufficiency and complete deficiency	Wang et al. Genome Res. 2011
Pancreatic neoplastic cysts	8 cyst resections	Recurrent mutations in components of ubiquitin-dependent pathways	Wu et al. PNAS 2011.
Gastric cancer	22 cases	Frequent mutation of ARID1A	Wang et al. Nat Genet 2011.
Prostate cancer	3 primaries 16 metastases	Recurrent alterations in TP53, DLK2, GPC6, and SDF4	Kumar et al. PNAS 2011

Conclusion and Outlook

Around 700 individual tumors representing 17 major cancer types were characterized in the studies above. That’s an astonishing number, but it’s only the tip of the iceberg. This year will see the publication of thousands or tens of thousands of cancer genomes/exomes. New genes and pathways will be identified. Mutational patterns will be revealed. Novel therapeutic targets will be suggested. I think that 2012 will be an exciting year for cancer genomics.

References
Ding L, Wendl MC, Koboldt DC, & Mardis ER (2010). Analysis of next-generation genomic data in cancer: accomplishments and challenges. Human Molecular Genetics, 19 (R2):R188-96. PMID: 20843826

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This entry was posted on Thursday, January 5th, 2012 at 12:53 pm by Dan Koboldt + and is filed under Cancer Genomics, Uncategorized. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.

6 comments

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zhao

I like your website and articles! It's very helpful!

Mona Spector

Hi Dan,

This is a great resource. Thanks for putting it together.

We have a paper published in Leukemia Dec 2011 on exome sequencing of a single case of mast cell leukemia. We found 2 somatic mutations that potentially impact therapeutic decisions for this rare form of leukemia.

Leukemia. 2011 Dec 16. doi: 10.1038/leu.2011.354.

I understand that you chose to limit the list to studies of multiple cases and our study does not fit that criteria. Just thought it would not hurt to ask if you would consider including our study in your compilation.

Best,

Mona

Ryan Morin

Thanks!

Dan Koboldt

Ryan, absolutely! I enjoyed your paper and apologize for the oversight - thank you for the reminder.

Ryan Morin

Hi Dan.

Nice compilation. I am unarguably biased in this matter, but I wonder if our paper on non Hodgkin lymphoma could also merit inclusion in the WGS list. 12 cases sequenced by WGS, 2 by exome and a total of 113 extension cases (RNA-seq).

Key findings: Mutation of MLL2 in 89% of FLs and 32% of DLBCL and mutations in MEF2B in 11.4% of DLBCL and 13.4% of FL.

Regards,

Ryan

Reference:

Morin, R.D., Mendez-Lago, M., Mungall, A.J., Goya, R., Mungall, K.L., Corbett, R.D., Johnson, N.A., et al., 2011. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature, 476(7360), pp.298–303.

Alfredo Hidalgo-Miranda

Great compilation!! You can also include the paper about non-Hodgkin by Morin et. al. in Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351.