Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy

Tamm, Erika; Cristofaro, Julie Di; Mazières, Stéphane; Pennarun, Erwan; Kushniarevich, Alena; Raveane, Alessandro; Semino, Ornella; Chiaroni, Jacques; Pereira, Luı́sa; Metspalu, Mait; Montinaro, Francesco

doi:10.1101/722165

Cited by 3 publications

(6 citation statements)

References 64 publications

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“…Two hundred twenty-two samples are presented here. Of these, 167 Italians and 6 Albanians were specifically selected and sequenced for this project with two versions (1.2 and 1.3) of the Infinium Omni2.5-8 Illumina beadchip, while 49 Italians and Europeans were genotyped with the Human660W-Quad BeadChip in the frame of another research (data file S1) ( 35 ) . Two separate worldwide datasets were prepared.…”

Section: Methodsmentioning

confidence: 99%

“…The sampling procedure and project aims related to these samples were reviewed and approved by the Ethics Committee for Clinical Experimentation of the University of Pavia, board minutes of 11 April 2013 and of 5 October 2010, respectively. Data for 49 samples from Italy and Europe were generated at the Institute of Genomics in Tartu and will be released in the accession link provided in ( 35 ). Requests for accessing previously published data should be directed to the corresponding authors of the publications where they were originally presented.…”

Section: Acknowledgmentsmentioning

confidence: 99%

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Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

et al. 2019

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European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non–steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

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Section: Methodsmentioning

confidence: 99%

Section: Acknowledgmentsmentioning

confidence: 99%

Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

et al. 2019

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“…QpWave and qpAdm in ADMIXTOOLSv4 . 1 package were used as in (19,90) by testing all the possible combinations of two, three and four sources on a set of target populations. We firstly used qpWave to establish, using f-statistics and a set of outgroups, whether the tested sources were significantly different and could be used to reconstruct the ancestry of a target population.…”

Section: Methodsmentioning

confidence: 99%

Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy

Raveane

Molinaro

Aneli

et al. 2022

Preprint

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Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithic transition and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidence points to demic and cultural influences between Southern Italians and the Balkans, starting with the initial Palaeolithic occupation until historical and modern times. To shed light on the dynamics of these contacts, we analysed a genome-wide SNP dataset of more than 700 individuals from the South Mediterranean area (102 from Southern Italy), combined with ancient DNA from neighbouring areas. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with the presence of a Bronze Age component ultimately originating from the Caucasus and characterised by high frequencies of Iranian and Anatolian Neolithic ancestries. Furthermore, to reveal possible signals of natural selection, we looked for extremely differentiated allele frequencies among Northern and Southern Italy, uncovering putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits, such as ALDH2, NID1 and CBLB.

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“…The final steps in the merger also include quality control measures which are specified by the user and sum up an extremely beneficial and time efficient module. Demo data [40][41][42] was not provided with Iliad for this submodule, although, example data can be freely obtained from the Estonian Biocentre (https://evolbio.ut.ee/). Example datafiles from published literature [40][41][42] were downloaded in Bed, Bim, and Fam Plink [43,44] formats from this site and converted into VCF files using Plink2 [43,44].…”

Section: Workflowmentioning

confidence: 99%

“…Demo data [40][41][42] was not provided with Iliad for this submodule, although, example data can be freely obtained from the Estonian Biocentre (https://evolbio.ut.ee/). Example datafiles from published literature [40][41][42] were downloaded in Bed, Bim, and Fam Plink [43,44] formats from this site and converted into VCF files using Plink2 [43,44]. Benchmarks are provided using this demo data (Table 3) to give users an insight into the resources required, and replication if needed.…”

Section: Workflowmentioning

confidence: 99%

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

Herrick,

Walsh

2023

Preprint

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Background: Processing raw genomic data for downstream applications such as imputation, association studies, and modeling requires numerous third-party bioinformatics software tools. It is highly time-consuming and resource-intensive with computational demands and storage limitations that pose significant challenges that increase cost. The use of software tools independent of one another, in a disjointed stepwise fashion, increases the difficulty and sets forth higher error rates because of fragmented job executions in alignment, variant calling, and/or build conversion complications. As sequencing data availability grows, the ability of biologists to process it using stable, automated, and reproducible workflows is paramount as it significantly reduces the time to generate clean and reliable data.Results: The Iliad suite of genomic data workflows was developed to provide users with seamless file transitions from raw genomic data to a quality-controlled variant call format (VCF) file for downstream applications. Iliad benefits from the efficiency of the Snakemake best practices framework coupled with Singularity and Docker containers for repeatability, portability, and ease of installation. This feat is accomplished from the onset with download acquisitions of any raw data type (FASTQ, CRAM, IDAT) straight through to the generation of a clean merged data file that can combine any user-preferred datasets using robust programs such as BWA, Samtools, and BCFtools. Users can customize and direct their workflow with one straightforward configuration file. Iliad is compatible with Linux, MacOS, and Windows platforms and scalable from a local machine to a high-performance computing cluster.Conclusion: Iliad offers automated workflows with optimized time and resource management that are comparable to other workflows available but generates analysis-ready VCF files from the most common datatypes using a single command. The storage footprint challenge of genomic data is overcome by utilizing temporary intermediate files before the final VCF is generated. This file is ready for use in imputation, genome-wide association study (GWAS) pipelines, high-throughput population genetics studies, select gene candidate studies, and more. Iliad was developed to be portable, compatible, scalable, robust, and repeatable with a simplistic setup, so biologists who are less familiar with programming can manage their own big data with this open-source suite of workflows.

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Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy

Cited by 3 publications

References 64 publications

Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

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