//The American Journal of Human Genetics

The American Journal of Human Genetics

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Articles of Interest

Chromosomal Haplotypes by Genetic Phasing of Human Families

Journal: The American Journal of Human Genetics | Year: 2011

Abstract:

Assignment of alleles to haplotypes for nearly all the variants on all chromosomes can be performed by genetic analysis of a nuclear family with three or more children. Whole-genome sequence data enable deterministic phasing of nearly all sequenced alleles by permitting assignment of recombinations to precise chromosomal positions and specific meioses. We demonstrate this process of genetic phasing on two families each with four children. We generate haplotypes for all of the children and their parents; these haplotypes span all genotyped positions, including rare variants. Misassignments of phase between variants (switch errors) are nearly absent. Our algorithm can also produce multimegabase haplotypes for nuclear families with just two children and can handle families with missing individuals. We implement our algorithm in a suite of software scripts (Haploscribe). Haplotypes and family genome sequences will become increasingly important for personalized medicine and for fundamental biology.

Peoples: - | Places: - | Topics: Deterministic phasing, Haploscribe, Haplotypes, and Parental phasing | DNA Type: Autosomal DNA

Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families

Journal: American Journal of Human Genetics | Year: 2016

Abstract:

The paternal haplogroup (hg) N is distributed from southeast Asia to eastern Europe. The demographic processes that have shaped the vast extent of this major Y chromosome lineage across numerous linguistically and autosomally divergent populations have previously been unresolved. On the basis of 94 high-coverage re-sequenced Y chromosomes, we establish and date a detailed hg N phylogeny. We evaluate geographic structure by using 16 distinguishing binary markers in 1,631 hg N Y chromosomes from a collection of 6,521 samples from 56 populations. The more southerly distributed sub-clade N4 emerged before N2a1 and N3, found mostly in the north, but the latter two display more elaborate branching patterns, indicative of regional contrasts in recent expansions. In particular, a number of prominent and well-defined clades with common N3a3’6 ancestry occur in regionally dissimilar northern Eurasian populations, indicating almost simultaneous regional diversification and expansion within the last 5,000 years. This patrilineal genetic affinity is decoupled from the associated higher degree of language diversity.

Peoples: | Places: Eurasia | Topics: | DNA Type: Y-DNA

Sequence Analysis of the Mitochondrial Genomes from Dutch Pedigrees with Leber Hereditary Optic Neuropathy

Journal: American Journal of Human Genetics | Year: 2003

Abstract:

The complete mitochondrial DNA (mtDNA) sequences for 63 Dutch pedigrees with Leber hereditary optic neuropathy (LHON) were determined, 56 of which carried one of the classic LHON mutations at nucleotide (nt) 3460, 11778, or 14484. Analysis of these sequences indicated that there were several instances in which the mtDNAs were either identical or related by descent. The most striking example was a haplogroup J mtDNA that carried the 14484 LHON mutation. Four different but related mitochondrial genotypes were identified in seven of the Dutch pedigrees with LHON, including six of those described by van Senus. The control region of the founder sequence for these Dutch pedigrees with LHON matches the control-region sequence that Macmillan and colleagues identified in the founder mtDNA of French Canadian pedigrees with LHON. In addition, we obtained a perfect match between the Dutch 14484 founder sequence and the complete mtDNA sequences of two Canadian pedigrees with LHON. Those results indicate that these Dutch and French Canadian 14484 pedigrees with LHON share a common ancestor, that the single origin of the 14484 mutation in this megalineage occurred before the year 1600, and that there is a 14484/haplogroup J founder effect. We estimate that this lineage—including the 14484 LHON mutation—arose 900–1,800 years ago. Overall, the phylogenetic analyses of these mtDNA sequences conservatively indicate that a LHON mutation has arisen at least 42 times in the Dutch population. Finally, analysis of the mtDNA sequences from those pedigrees that did not carry classic LHON mutations suggested candidate pathogenic mutations at nts 9804, 13051, and 14325.

Peoples: | Places: | Topics: Leber’s Hereditary Optic Neuropathy | DNA Type: mtDNA

Inheritance of Mitochondrial DNA Recombinants in Double-Heteroplasmic Families: Potential Implications for Phylogenetic Analysis

Journal: The American Journal of Human Genetics | Year: 2007

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

Phylogeny of East Asian Mitochondrial DNA Lineages Inferred from Complete Sequences

Journal: The American Journal of Human Genetics | Year: 2003

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

Somatic Mutations throughout the Entire Mitochondrial Genome Are Associated with Elevated PSA Levels in Prostate Cancer Patients

Journal: The American Journal of Human Genetics | Year: 2010

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

Mitochondrial DNA Haplogroups M7b1′2 and M8a Affect Clinical Expression of Leber Hereditary Optic Neuropathy in Chinese Families with the m.11778G→A Mutation

Journal: The American Journal of Human Genetics | Year: 2008

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

Maternal History of Oceania from Complete mtDNA Genomes: Contrasting Ancient Diversity with Recent Homogenization Due to the Austronesian Expansion

Journal: The American Journal of Human Genetics | Year: 2014

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

A Highly Unstable Recent Mutation in Human mtDNA

Journal: The American Journal of Human Genetics | Year: 2013

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

Analysis of Mitochondrial DNA Diversity in the Aleuts of the Commander Islands and Its Implications for the Genetic History of Beringia

Journal: The American Journal of Human Genetics | Year: 2002

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

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