BACKGROUND: DNA palindromes are a unique pattern of repeat sequences that are present in the @entity1 genome. It consists of a sequence of @entity2036 in which the second half is the complement of the first half but appearing in reverse order. These palindromic sequences may have a significant role in DNA replication, transcription and gene regulation processes. They occur frequently in @entity1 @entity5 by clustering at specific locations of the genome that undergo gene amplification and tumorigenesis. Moreover, some studies showed that palindromes are clustered in amplified regions of @entity0 genomes especially in chromosomes (chr) 8 and 11. With the large number of personal genomes and @entity5 genomes becoming available, it is now possible to study their association to diseases using computational methods. Here, we conducted a pilot study on chromosomes 8 and 11 of @entity5 genomes to identify computationally the differentially occurring palindromes. METHODS: We processed 69 @entity0 genomes from The Cancer Genome Atlas including serum-normal and @entity5 genomes, and 1000 Genomes to serve as control group. The Biological Language Modelling Toolkit (BLMT) computes palindromes in whole genomes. We developed a computational pipeline integrating BLMT to compute and compare prevalence of palindromes in personal genomes. RESULTS: We carried out a pilot study on @entity42732 and chr 11 taking into account single nucleotide polymorphisms, insertions and deletions. Of all the palindromes that showed any variation in @entity5 genomes, 38% of what were near @entity0 genes happened to be the most differentiated palindromes in @entity5 (i.e. they ranked among the top 25% by our heuristic measure). CONCLUSIONS: These results will shed light on the prevalence of palindromes in oncogenes and the mutations that are present in the palindromic regions that could contribute to genomic rearrangements, and @entity0 progression.

A pilot study on the prevalence of DNA palindromes in XXXX genomes.

@entity1 :: ('9606', 'Species') :: ['human'] @entity0 :: ('MESH:D001943', 'Disease') :: ['breast cancer'] @entity2036 :: ('MESH:D009711', 'Chemical') :: ['nucleotides'] @entity5 :: ('MESH:D009369', 'Disease') :: ['tumor', 'cancers', 'cancer'] @entity42732 :: ('MESH:C040118', 'Chemical') :: ['chr 8']
@entity0 :: (MESH:D001943,Disease) :: ['breast cancer']
