Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp. Inflammatory bowel disease (IBD) is a modern lifestyle disease with a worldwide prevalence. IBD involves mainly Crohn's disease (CD) and ulcerative colitis (UC) the etiology of which differs, so the clinical determination of the disease is difficult. Chronic inflammation of the gastrointestinal tract defined as cycling of the acute inflammation phase and remission is typical for IBD, both CD and UC. While in UC the disease is specifically localized to the colon with different degree of continuous inflammation proximally from the rectum, the CD can manifest anywhere in the gut. To date, there is no clear evidence of a single factor causing the IBD. It is affected by genetic susceptibility, microbiome composition, immune response dysregulation as well as various environmental factors 1. The vitD defficiency is common among IBD patients 2,3 and it has been speculated, that a low level of vitD might be one of the risk factors influencing the IBD 4-6. The current epidemiological studies of IBD show and upward dynamics in countries distant from the equator 7 , strongly suggesting a correlation between IBD incidence

Low-coverage massively parallel genome sequencing for non-invasive prenatal testing (NIPT) of common aneuploidies is one of the most rapidly adopted and relatively low-cost DNA tests. Since aggregation of reads from a large number of samples allows overcoming the problems of extremely low coverage of individual samples, we describe the possible re-use of the data generated during NIPT testing for genome scale population specific frequency determination of small DNA variants, requiring no additional costs except of those for the NIPT test itself. We applied our method to a data set comprising of 1,548 original NIPT test results and evaluated the findings on different levels, from in silico population frequency comparisons up to wet lab validation analyses using a gold-standard method. The revealed high reliability of variant calling and allelic frequency determinations suggest that these NIPT data could serve as valuable alternatives to large scale population studies even for smaller countries around the world. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature methods frequencies of variants in our sample set and six different ExAC populations. Results are shown separately for (a) SNVs based on 68,326 variants; and (b) indels based on 2,909. In both cases, only those variants were used, which were simultaneously identified in each data subset with MAF higher than 5%. AFR = African/African American, AMR = American (Latino), EAS = East Asian, FIN = Finnish, NFE = Non-Finnish European, SAS = South Asian, SVK = Slovak. 2 7 SupplementaryTable 1 (uploaded as a separate Excel sheet of the Supplementary Table file):List of variants identified in the region of the CLCN1 (chloride voltage-gated channel 1, OMIM * 118425) gene in ExAC populations, dbSNP and in our data set. Only 17 of them had ExAC frequencies above 5% (highlighted in yellow). All but five were identified in our data set too with very similar calculated population frequencies. The exceptions, rs34904831, rs191902231, rs182668076, rs2280663 and rs73726622, were found to have ExAC frequencies +/-5% (depending on population). Originally three of these variants were identified in our data set too, although they were filtered out due slightly lower than 5% frequency (Suppl.Tab.1), further suggesting the feasibility of lowering our frequency restrictions. Our data contained also 89 variants missing from ExAC (highlighted in red), but found to have each of them deep intronic positions falling outside ExAC´s BED file. AFR = African/African American, AMR = American, EAS = East Asian, FIN = Finnish, NFE = Non-Finnish European, SAS = South Asian, SVK = Slovak. Supplementary Table 2 (uploaded as a separate Excel sheet of the Supplementary Table file): Verification of 87 positions in five polymorphic genomic loci of 58 randomly selected samples of our sample set from which genomic DNA was available to validation purposes. Reads from positions covered by multiple reads in individual samples (such in case of sample ID4730, where both alleles we...

Supplementary data are available at Bioinformatics online.