Virmid: accurate detection of somatic mutations with sample impurity inference

Kim, Sangwoo; Jeong, Kyowon; Bhutani, Kunal; Lee, Jehee; Patel, Amit K.; Scott, Eric; Nam, Hojung; Lee, Hayan; Gleeson, Joseph G.; Bafna, Vineet

doi:10.1186/gb-2013-14-8-r90

Cited by 61 publications

(49 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…[55][56][57][58][59] However, in vivo modeling of somatic mutations in the developing brain has been challenging given the limitations of genome-editing tools 60 and the size constraints of viral vectors. 61 In the present study, we combined in utero electroporation with the CRISPR-Cas9 system to introduce somatic genome modifications in a small fraction of neurons in the developing brain.…”

Section: Discussionmentioning

confidence: 99%

Somatic Mutations in TSC1 and TSC2 Cause Focal Cortical Dysplasia

Lim

Gopalappa

Kim

et al. 2017

The American Journal of Human Genetics

Self Cite

161

159

View full text Add to dashboard Cite

Focal cortical dysplasia (FCD) is a major cause of the sporadic form of intractable focal epilepsies that require surgical treatment. It has recently been reported that brain somatic mutations in MTOR account for 15%-25% of FCD type II (FCDII), characterized by cortical dyslamination and dysmorphic neurons. However, the genetic etiologies of FCDII-affected individuals who lack the MTOR mutation remain unclear. Here, we performed deep hybrid capture and amplicon sequencing (read depth of 1003-20,0123) of five important mTOR pathway genes-PIK3CA, PIK3R2, AKT3, TSC1, and TSC2-by using paired brain and saliva samples from 40 FCDII individuals negative for MTOR mutations. We found that 5 of 40 individuals (12.5%) had brain somatic mutations in TSC1 (c.64C>T [p.Arg22Trp] and c.610C>T [p.Arg204Cys]) and TSC2 (c.4639G>A [p.Val1547Ile]), and these results were reproducible on two different sequencing platforms. All identified mutations induced hyperactivation of the mTOR pathway by disrupting the formation or function of the TSC1-TSC2 complex. Furthermore, in utero CRISPR-Cas9-mediated genome editing of Tsc1 or Tsc2 induced the development of spontaneous behavioral seizures, as well as cytomegalic neurons and cortical dyslamination. These results show that brain somatic mutations in TSC1 and TSC2 cause FCD and that in utero application of the CRISPR-Cas9 system is useful for generating neurodevelopmental disease models of somatic mutations in the brain.

show abstract

Section: Discussionmentioning

confidence: 99%

Somatic Mutations in TSC1 and TSC2 Cause Focal Cortical Dysplasia

Lim

Gopalappa

Kim

et al. 2017

The American Journal of Human Genetics

Self Cite

161

159

View full text Add to dashboard Cite

show abstract

“…The detailed sequence of primer and index are listed in Supplementary Bioinformatic analysis. We used both the Virmid (http://sourceforge.net/ projects/virmid/) and MuTect (http://www.broadinstitute.org/cancer/cga/ mutect) algorithms to jointly analyze blood-brain paired WES data sets and call any given variants that arise de novo in affected brains (not in the germline) 12,13 . Although both tools are useful for finding somatic mutations with low-allelic fraction in genetically heterogeneous samples, they are based on different probability models emerged from independent approaches.…”

Section: Mouse Care and Informationmentioning

confidence: 99%

“…To detect somatic mutations in the affected brains, we used two recently developed algorithms, Virmid (http://sourceforge.net/projects/virmid/) and MuTect (http://www. broadinstitute.org/cancer/cga/mutect), which are particularly useful Brain somatic mutations in MTOR cause focal cortical dysplasia type II leading to intractable epilepsy for detecting somatic mutations with low allelic frequencies in genetically heterogeneous tissues 12,13 .…”

mentioning

confidence: 99%

Brain somatic mutations in MTOR cause focal cortical dysplasia type II leading to intractable epilepsy

Lim

Kim

Kang

et al. 2015

Nat Med

Self Cite

418

408

View full text Add to dashboard Cite

Focal cortical dysplasia type II (FCDII) is a sporadic developmental malformation of the cerebral cortex characterized by dysmorphic neurons, dyslamination and medically refractory epilepsy. It has been hypothesized that FCD is caused by somatic mutations in affected regions. Here, we used deep whole-exome sequencing (read depth, 412-668×) validated by site-specific amplicon sequencing (100-347,499×) in paired brain-blood DNA from four subjects with FCDII and uncovered a de novo brain somatic mutation, mechanistic target of rapamycin (MTOR) c.7280T>C (p.Leu2427Pro) in two subjects. Deep sequencing of the MTOR gene in an additional 73 subjects with FCDII using hybrid capture and PCR amplicon sequencing identified eight different somatic missense mutations found in multiple brain tissue samples of ten subjects. The identified mutations accounted for 15.6% of all subjects with FCDII studied (12 of 77). The identified mutations induced the hyperactivation of mTOR kinase. Focal cortical expression of mutant MTOR by in utero electroporation in mice was sufficient to disrupt neuronal migration and cause spontaneous seizures and cytomegalic neurons. Inhibition of mTOR with rapamycin suppressed cytomegalic neurons and epileptic seizures. This study provides, to our knowledge, the first evidence that brain somatic activating mutations in MTOR cause FCD and identifies mTOR as a treatment target for intractable epilepsy in FCD.

show abstract

“…Prepared library was sequenced by HiSeq2000 (Illumina). Sequenced data were analyzed by Virmid to detect somatic mutations (18).…”

Section: Real-time Reverse-transcription Pcr (Rt-pcr)mentioning

confidence: 99%