ArticleBioinformatics (Oxford, England)2013
A genomic random interval model for statistical analysis of genomic lesion data.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- The genomic landscape of relapsed infant and childhood KMT2A-rearranged acute leukemia.Nature communications · 2025Article
- Patterns and variations of copy number alterations in acute myeloid leukemia: insights from the LeukAtlas database.Leukemia · 2025Article
- A new genomic framework to categorize pediatric acute myeloid leukemia.Nature genetics · 2024Article
- Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The genomic landscape of pediatric acute lymphoblastic leukemia.Nature genetics · 2022Article
- Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia.Blood cancer discovery · 2022Article
- The acquisition of molecular drivers in pediatric therapy-related myeloid neoplasms.Nature communications · 2021Article
- Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations.Nature communications · 2020Article
- Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia.Blood cancer discovery · 2020Article
- Large-scale analysis of acquired chromosomal alterations in non-tumor samples from patients with cancer.Nature biotechnology · 2020Article
- Genomic subtyping and therapeutic targeting of acute erythroleukemia.Nature genetics · 2019Article
- Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours.Nature · 2018Article
- The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias.Nature genetics · 2015Article
- Genomic landscape of paediatric adrenocortical tumours.Nature communications · 2015Article
- Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma.Cell reports · 2014Article
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Authors and funding
6 authors.
Funding
Abstract
motivationTumors exhibit numerous genomic lesions such as copy number variations, structural variations and sequence variations. It is difficult to determine whether a specific constellation of lesions observed across a cohort of multiple tumors provides statistically significant evidence that the lesions target a set of genes that may be located across different chromosomes but yet are all involved in a single specific biological process or function.
resultsWe introduce the genomic random interval (GRIN) statistical model and analysis method that evaluates the statistical significance of the abundance of genomic lesions that overlap a specific locus or a pre-defined set of biologically related loci. The GRIN model retains certain biologically important properties of genomic lesions that are ignored by other methods. In a simulation study and two example analyses of leukemia genomic lesion data, GRIN more effectively identified important loci as significant than did three methods based on a permutation-of-markers model. GRIN also identified biologically relevant pathways with a significant abundance of lesions in both examples. AVAILABILITY: An R package will be freely available at CRAN and www.stjuderesearch.org/site/depts/biostats/software.
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