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JOGG, Fall 2010
« : 28 Декабрь 2010, 00:25:13 »

Columns, Editorials, and Features

Editor's Corner
JoGG 2.0
Blaine T. Bettinger

'Satiable Curiosity
Up Hill and Down Dale in the Genomic Landscape:
The Odd Distribution of Matching Segments
Ann Turner
PDF                  Segments Data File


Letter to JoGG re: Y-STR Mountains in Haplospace,
Part II: Application to Common Polish Clade
Peter S. Gwozdz, Lawrence Mayka, Michael Konczak, and Thomas Krahn


Phasing the Chromosomes of a Family Group
When One Parent is Missing
T. Whit Athey

Centre-Based Hard and Soft Clustering Approaches
for Y-STR Data
Ali Seman, Zainab Abu Bakar, and Azizian Mohd. Sapawi

mtDNA Haplogroup T Phylogeny Based on Full
Mitochondrial Sequences
David A. Pike, Terry J. Barton, Sjana L. Bauer, and Elizabeth
(Blake) Kipp
PDF                  Quick Reference Quide to mtDNA Haplogroup T

A Reference Database to Support Analysis of mtDNA Haplogroup N,
its Descendant Haplogroups, and Associated Clades
Jim Logan and Whit Athey

Review Article

Revealing American Indian and Minority Heritage Using
Y-line, Mitochondrial, Autosomal and X-Chromosomal
Testing Data Combined with Pedigree Analysis
Roberta Estes

Special Section:  Y-DNA Projects

Clan, Tribe and Household:
Y-DNA & One Name Studies
Francois Andre Greeff, Andre Servaas Greeff,
Yolanda Harris, Lucas Rinken, and Dawid Welgemoed

Towards Improvement in Y-DNA Surname
Project Administration
James M. Irvine

Defining a Methodology to Reconstruct the
Family Trees of a Surname Within a
DNA/Documentary Dual Approach Project
Chris Pomery

Larkin DNA Project - Ancestral Parish Sampling
on the Shannon River
Bradley T. Larkin
PDF                  Larkin Data File

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Re: JOGG, Fall 2010
« Ответ #1 : 28 Декабрь 2010, 01:00:15 »
Ну вот, как я предполагал, Тернер указывает на консервативность региона MHC-HLA региона, что оказывает влияние на качество и количество УПС-сегментов, детектируемых в этом регионе FamFinder,RelFinder,AncFinder-ом.

Chromosome 6 houses a set of genes known collectively as the Major Histocompatibility Complex., important for the immune system’s role of distinguishing the self from a foreign invader. The genes, including the HLA (Human Leukocyte Antigen) genes tested for organ transplant compatibility, are densely packed into a region of about 3,600,000 bases (3.6 Mb) at positions 29,750,000 to 33,100,000. They harbor an enormous amount of variability, yet paradoxically, the recombination rate is low. Consequently, variants in different parts of the MHC often travel together as a package, a haplotype.* As a consequence, a “conserved extended haplotype” may occur in large numbers of people. A recent study showed that the single most common haplotype was found in 8.7% of the subjects, and the ten most common haplotypes accounted for 30% .4 From a genetic genealogist’s perspective, similarities in this region may be too general to have utility in identifying recent relationships. However, if the number of matches in the region is on the low side compared to most people, the haplotype may be more distinctive and thus more informative.
Because of these biological underpinnings, it is quite possible that the peak on chromosome 6 will survive even after merging larger numbers of records. Will other peaks also stand out, or will they be eroded into flat valleys along the Y = 1 line? There are other candidates. Although the term “conserved extended haplotype” seems to be associated specifically with the MHC, the concept could apply to other regions. For instance, an inversion around the centromere of chromosome 9 may have reduced variability, since it does not align well with the more common version during the recombination process.


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