{"action":"created","issue":{"url":"https://api.github.com/repos/UCSC-Treehouse/operations/issues/22","repository_url":"https://api.github.com/repos/UCSC-Treehouse/operations","labels_url":"https://api.github.com/repos/UCSC-Treehouse/operations/issues/22/labels{/name}","comments_url":"https://api.github.com/repos/UCSC-Treehouse/operations/issues/22/comments","events_url":"https://api.github.com/repos/UCSC-Treehouse/operations/issues/22/events","html_url":"https://github.com/UCSC-Treehouse/operations/issues/22","id":193681141,"number":22,"title":"Repository - EGAD00001001098 Infant MLL-rearranged 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+ QC","description":null,"creator":{"login":"klearned","id":23464751,"avatar_url":"https://avatars.githubusercontent.com/u/23464751?v=3","gravatar_id":"","url":"https://api.github.com/users/klearned","html_url":"https://github.com/klearned","followers_url":"https://api.github.com/users/klearned/followers","following_url":"https://api.github.com/users/klearned/following{/other_user}","gists_url":"https://api.github.com/users/klearned/gists{/gist_id}","starred_url":"https://api.github.com/users/klearned/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/klearned/subscriptions","organizations_url":"https://api.github.com/users/klearned/orgs","repos_url":"https://api.github.com/users/klearned/repos","events_url":"https://api.github.com/users/klearned/events{/privacy}","received_events_url":"https://api.github.com/users/klearned/received_events","type":"User","site_admin":false},"open_issues":4,"closed_issues":0,"state":"open","created_at":"2016-12-06T19:14:44Z","updated_at":"2016-12-19T18:29:56Z","due_on":null,"closed_at":null},"comments":13,"created_at":"2016-12-06T04:34:13Z","updated_at":"2016-12-21T22:22:06Z","closed_at":null,"body":"Original Paper: [PMC4553269](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4553269/)\r\nFrom: St. Jude (via EGA: [EGAD00001001098](https://www.ebi.ac.uk/ega/datasets/EGAD00001001098))\r\nDetailed file spreadsheet: [EGAD00001001098 PCGP: infant MLL-rearranged ALL](https://docs.google.com/a/ucsc.edu/spreadsheets/d/1nCUctVIyqIbp9EGtT0Tz1KMfCchWU3-GJqepvxFjnpo/edit?usp=sharing)\r\n\r\n**Task List:**\r\n- [x] Request permission\r\n- [x] Download & decrypt data (12/3/16)\r\n- [x] Convert bam to fastq\r\n- [ ] Treeshop (RNAseq Pipeline + QC)\r\n\r\n**Important paper excerpts:**\r\n\r\n> **DESIGN DESCRIPTION**\r\n> Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia subtype with a poor prognosis. To define its mutational landscape, we performed whole genome, exome, RNA sequencing and targeted DNA sequencing on leukemic cells from 65 infants (47 MLL-R and 18 non-MLL-R) and 20 older children (MLL-R). Our data demonstrated infant MLL-R ALL to have one of the lowest frequencies of somatic mutations of any cancer sequenced to date, with the predominant leukemic clone carrying a mean of only 1.3 non-silent mutations per case. Despite the paucity of mutations, activating mutations in tyrosine kinases, phosphatidylinositol-3-kinase and RAS pathway genes, were detected in 47% of cases, including a novel internal tandem duplication in PIK3R1 shown to activate the PI-3K pathway. Surprisingly, however, these mutations were often present in only a minor sub-clone and were frequently lost at the time of relapse. In contrast to infant cases, MLL-R leukemia in older children had a greater number of somatic mutations (a mean of 6.5/case versus 1.3/case, P=7.15x10-5) and contained frequent mutations (45%) in epigenetic regulators, a category of genes that with the exception of MLL was rarely mutated in infant MLL-R ALL.\r\n\r\n> **RNA Sequencing**\r\n> RNA sequencing was performed on 21 diagnostic and 2 paired relapse cases from the discovery cohort (not INF007), 12 diagnostic and 4 relapse MLL-R infant ALLs and 6 non–MLL-R infants from the validation cohort, and on 18/20 cases from the non-infant MLL-R cohort (Supplementary Tables 9–11). Total RNA was extracted with Trizol (Ambion) per manufacturer’s protocol. One microgram of total RNA was DNase I (Ambion) treated at room temperature for 15 minutes followed by phenol/chloroform/isoamyl extraction and ethanol precipitation. The integrity of the DNase I treated RNA was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies,) prior to poly-A mRNA selection. Poly-A mRNA selection and subsequent cDNA synthesis was done using Illumina TruSeq RNA sample preparation kit according to manufacturer’s protocol. The cDNA was fragmented (200bp peak) with a Covaris E210 ultrasonicator prior to library preparation utilizing Illumina TruSeq RNA sample preparation kit according to manufacturer’s protocol. The adapter ligated fragments were PCR amplified for 10 cycles. The quality and size of the final library preparation was analyzed on the Agilent 2100 Bioanalyzer. Sequencing was performed on the Illumina HiSeq2500 in rapid mode to generate paired end 100 cycle reads. Putative in-frame fusions were validated by RT-PCR followed by Sanger sequencing. Primer sequences are available upon request."},"comment":{"url":"https://api.github.com/repos/UCSC-Treehouse/operations/issues/comments/268658395","html_url":"https://github.com/UCSC-Treehouse/operations/issues/22#issuecomment-268658395","issue_url":"https://api.github.com/repos/UCSC-Treehouse/operations/issues/22","id":268658395,"user":{"login":"adurbin2","id":20465314,"avatar_url":"https://avatars.githubusercontent.com/u/20465314?v=3","gravatar_id":"","url":"https://api.github.com/users/adurbin2","html_url":"https://github.com/adurbin2","followers_url":"https://api.github.com/users/adurbin2/followers","following_url":"https://api.github.com/users/adurbin2/following{/other_user}","gists_url":"https://api.github.com/users/adurbin2/gists{/gist_id}","starred_url":"https://api.github.com/users/adurbin2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adurbin2/subscriptions","organizations_url":"https://api.github.com/users/adurbin2/orgs","repos_url":"https://api.github.com/users/adurbin2/repos","events_url":"https://api.github.com/users/adurbin2/events{/privacy}","received_events_url":"https://api.github.com/users/adurbin2/received_events","type":"User","site_admin":false},"created_at":"2016-12-21T22:22:06Z","updated_at":"2016-12-21T22:22:06Z","body":"@rcurrie is this one running, or maybe waiting for core?"}}
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