EGAGenomicsOtherhttps://ega-archive.org/studies/EGAS00001000532EGAEGA study EGAS00001000532Sardinian Chromsome Y 2012 AnalysisEGArestricted<h4>Background</h4>Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions.<h4>Methods</h4>DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software.<h4>Results</h4>From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region.<h4>Conclusions</h4>The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome.Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample.Francalacci Paolo P, Sanna Daria D, Useli Antonella A, Berutti Riccardo R, Barbato Mario M, Whalen Michael B MB, Angius Andrea A, Sidore Carlo C, Alonso Santos S, Tofanelli Sergio S, Cucca Francesco Fprophase chromosome, chromatid, Chromosome, Sardinia., interphase chromosomeHuman, sample., human being, Man (Taxonomy), Homo sapiens, Chromosome, Modern Man, Modern, Y, Man, Y Chromosomes, human, Chromosomes, sample populationeIF2C2, SEL-10, hCdc4, human being, ago, 1110001A17Rik, l(2)k08121, AGO 2, l(2)04845, Y Chromosomes, Chromosomes, MRE20, Human, FBXW3, FBXW6, School-Age, Northern Europe, Homo sapiens, CG7439, (2Z)-but-2-enedioate, Southern Europe, Man, male, School-Age Populations, Diversity, Genetic, Man (Taxonomy), mitochondrial genome, dAGO2, dAGO1, Y, Population, FBW6, l(2)4845, FBW7, Fbw7, genetic, Fbxo30, ago2, Sardinia, ago1, SEL10, dAgo1, CDC4, dAgo2, Cdc4, FBXO30, Fbx30, Dm Ago1, Ago2, School Age Population, Ago1, Nucleotide, constitutitional genetic, Variation, cdc4, Genetic Variations, FBX30, DmelCG7439, Variations, ago1-1, Ago-1, Ago-2, Dm Ago2, Mitochondrial DNA, Males, RnBP, DmFbw7, DmelCG15010, Modern, familial, anon-WO0257455.29, anon-WO0118547.345, GlcNAc 2-epimerase, Diversities, Tree, Fbwd6, N-acetyl-D-glucosamine 2-epimerase, CG6671, School Age, RENBP, Genetic Diversities, Western Europe, hAgo, Fbxw6, AG02, l(2)k00208, nucleotides, CG13452, Populations, mtDNA, maleate, Genetic Diversity, School Age Populations, human, AGE, male human body, mitochondrial DNA, Ago, Chromosome, AGO, ago-2, Modern Man, SCF[Ago], Mitochondrial DNA., renin-binding protein, CG15010, inherited genetic, School-Age Population, hereditary, DmelCG6671Networks, Previously, Transposed, Nucleotide Sequencing, Approximate, determination, Massively-Parallel, MBP-C, Blood, adult stage, Phylogenetic Structure, Transposition, Significant, MBP1, REMOVAL, No Information, Phylogenetic Analysis, INCLUSION, Y Chromosomes, Portion, Phylogenetic Signals, Sardinian Language, Data Not Available, Techniques, High-Throughput RNA Sequencing, Phylogenetic Inference, Method, Light Emitting Diode, Statistical Significance, Molecular Phylogenetics, Comparative Analysis, Software Engineering, Part, Analysis, Phylogenetic Comparative Analysis, (2Z)-but-2-enedioate, Consortium, Contains, adult, Computer Program, Phylogenetic Relationship, Deep Sequencing, INSL3R, male, HSMBPC, Eosinophil granule major basic protein, Centers, Group, Not Classified, thymus nucleic acid, me75, Phylogenomic, Man (Taxonomy), Illumina Sequencing, statistically significant, Molecular, Open, Computer Programs and Programming, chromatid, procedures, Myelin membrane encephalitogenic protein, Y, Sardinian, Comprise, Phylogenetic Networks, D17Mit170, T1, inclusion criteria, GREAT, geographical area, High Throughput RNA Sequencing, Methodological Studies, Adverse Event Conditionally Related to Intervention, Had, Phylogenetic Network, Familiar, MBPD, Network Interface, Phylogenetic Reconstructions, Great, Pregnancy-associated major basic protein, Usefulness, Phylogenetic Incongruences, Double-Stranded DNA, EXTRACTING, Phylogenetic Clustering, deoxyribonucleic acids, DNAn, Paternal Relative, Relationship, Nucleotide, Has, INCREASED, TP, High-Throughput RNA, Phylogenetic Comparative Method, and Consortia, Phylogenetic Analyse, Doubling, Modern, Genome Sequencing, High-Throughput DNA Sequencing, Phylogenetic Inferences, Double-Stranded, Procedure, Tl3, Phylogenetic Analyses, Tl2, Source Softwares, results, Significance, Phylogenetic Generalized Least Squares, Extracted, Software Tools, Programs, Contained, (Deoxyribonucleotide)n+m, UNCLASSIFIED, Program, Computer Applications, mld, Ion Torrent Sequencing, Complete Genome, informative, significant, Non, NON, Massively-Parallel Sequencing, C76307, Computer Applications Software, About, Next-Generation, Computer Applications Softwares, Not, Conditionally Related to Intervention, Phylogenetic Comparative Analyses, Ion Torrent, shi, Hmbpr, Softwares, DNA Sequence, desoxyribose nucleic acid, Phylogenetic Incongruence, Adults, Deviation, nucleotides, LGR8, statistical significance, Inclusion, Light Emitting Diode Device, Lgr8, Software Applications, VARIATION, positional polypeptide feature, Phylogenetic Tree, maleate, NO INFORMATION, Source Software, TRANSPOSED, Network Device, Phylogenies, EMBP, Methodological, No Information Available, Methodological Study, human, Unclassified Attribution, Unclassified Abnormality, High Throughput Sequencing, Extracted Lead, Phylogenetic Trees, Applications, Chromosome, Comparative Method, Clustering, PBMCs, ds DNA, Phylogenetic Groups, Myelin A1 protein, Unclassified, Y., DNA, Previous, Delivery, Nucleotide Sequence, Community, Computer Software Applications, Nearly, Inclusion Criteria, Non-, High Throughput DNA Sequencing, human being, DNS, Phylogenetic Reconstruction, Procedures, (Deoxyribonucleotide)n, region or site annotation, R75289, Consortium or Network, number, High-Throughput DNA, Network, Computer, Informative, Illumina, Chromosomes, Next-Generation Sequencing, Deoxyribonucleic acids, Distance, Phylogenomics, Human, COLEC1, Phylogenetic Comparative Methods, Conditional Attribution, Deoxyribonucleic Acid, Information Not Available, Inference, Homo sapiens, Deep, Transpose, PBMC, Relatedness, Studies, Variant, Phylogenetic Relatednesses, Low, Phylogenetic Relatedness, Massively Parallel Sequencing, Useful, Technique, Man, Application, NCI Consortium or Network, Community Phylogenetics, study, Open Source Softwares, positional, Negation, Complete, Ion Proton Sequencing, Whole Genome, Gpr106, Birth, Inclusions, Software Application, Complete Genome Sequencing, Signal, Open Source Software, Double Stranded, Former, Proteoglycan 2, RXFPR2, Deoxyribonucleic acid, MBL, Pyrosequencing, MBP, Contain, Phylogenetic Distances, Structure, Sequencing, Almost, Computer Software Application, Heightened, Reconstruction, Study, Sardinia, NO ANSWER PROVIDED, Tools, Statistically Significant, Whole, High-Throughput, RNA Sequencing, Phylogenetic Distance, Incongruence, (Deoxyribonucleotide)m, Approximately, Born, LED (Light Emitting Diode), Known, GPR106, Including, Variation, Possess, Applications Software, FORMER, Open Source, SINGLE, Molecular Phylogenetic, Computer Software, cou, whole blood, Include, Males, DNAn+1, Conditional/Unclassified, Inclusion Bodies, Tree, Extraction, Phylogenetic Comparative, BMPG, Phylogenetic Clusterings, Tool, Sequences, prophase chromosome, Software Tool, Lr, Inclusion Body, Have, Sequence, DNA Sequencing, Double, chemical analysis, sequence, MBL2D, background, techniques, ds-DNA, Software, NI, Next Generation Sequencing, Single Person, SRD, EXTRACTED, Phylogenetic Group, Peripheral Blood, interphase chromosome, Increased, Engineering, Containing, Phylogenetic Signal, Phylogenetic Structures, LGR8.1, golli-mbp, No Data, Negated, NON Mouse, primary structure of sequence macromolecule, introduction, male human body, Specified, Reticuloendothelial System, Analyse, Computer Programs, No, Applications Softwares, Phylogenetic, High-Throughput Sequencing, Only, LED, Increase, Specific, Modern Man, cardinality, Community Phylogenetic, Desoxyribonukleinsaeure, Bra, Phylogenetic Relationships, High Throughput Nucleotide Sequencing, Solitary, Inclusive, Single, assay, No Data Available, Paternal, Ion Proton, Alone, High-Throughput Nucleotide, methodology, paternalfalseChromosome Y Philogeny in SardiniaGenetic variation within the male specific portion of the Y chromosome (MSY) can clarify the origins of contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing of 1,204 Sardinian males identified 11,763 MSY single nucleotide polymorphisms (SNPs), of which 6,751 have not previously been observed. We constructed a MSY phylogenetic tree containing all main haplogroups found in Europe along with many Sardinian-specific lineage clusters within each haplogroup. The tree was calibrated with archaeological data from the initial expansion of the Sardinian population ~7,700 years ago. The ages of nodes highlight different genetic strata in Sardinia and reveal presumptive timing of coalescence with other human populations. We calculate a putative age for coalescence of ~180-200,000 years ago, consistent with previous mitochondrial DNA (mtDNA) based estimates.2017-07-26 15:39:25EGAS00001000532960625926048EGAD00001000618EGAC00001000121