Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system

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A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe

Peer reviewe

Additional file 1: of Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system

Figure S1. Representative Sanger electropherograms of the generated homopolymers. 4-mers, 5-mers, and 6-mers are shown in the left, middle, and right columns, respectively. (PDF 176 kb

Additional file 2: of Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system

Table S1. Mutagenesis, amplification and sequencing primers in the plasmid system. Amplification/sequencing primers contain a starting “Tag sequence,” which was separated by a space within the primer sequence. (DOCX 35 kb

Additional file 5: of Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system

Table S2. Self-designed primers used for assessing HP regions in the CFTR gene. Flopping bases on known SNPs are in brackets. “Tag sequences” also included in the beginning of the primers, separated by a space. (DOCX 58 kb

Additional file 4: of Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system

Figure S3. Sanger electropherogram of a sample of a patient with a CFTR 2184insA mutation in heterozygous form. (PDF 45 kb

Additional file 6: of Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system

Table S3. Self-designed primers used for assessing non- HP regions in the CFTR gene. “Tag sequences” also included in the beginning of the primers, separated by a space. (DOCX 31 kb

Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity

Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country's complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a region from northeastern Italy, which is known for isolated communities. Total of 1310 samples, collected from six geographically isolated villages, were genotyped at >145000 single-nucleotide polymorphism positions. Newly genotyped data were analyzed jointly with the available genome-wide data sets of individuals of European descent, including several population isolates. Despite the linguistic differences and geographical isolation the village populations still show the greatest genetic similarity to other Italian samples. The genetic isolation and small effective population size of the village populations is manifested by higher levels of genomic homozygosity and elevated linkage disequilibrium. These estimates become even more striking when the detected substructure is taken into account. The observed level of genetic isolation in Friuli-Venezia Giulia region is more extreme according to several measures of isolation compared with Sardinians, French Basques and northern Finns, thus proving the status of an isolate