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Inside the human genome : a case for non-intelligent design
How do you explain flaw in a world engineered by God? Avise extends this age-old question to the most basic aspect of humanity's physical evidence-- our genes-- and provides the evolutionary answers.
Book
Dynamics of CAG repeat loci revealed by the analysis of their variability
In order to understand the dynamics of the expressed single tandem repeat trinucleotides (most of them involved in pathological expansion), the diversity in 10 different loci (SCA1, SCA2, SCA3, SCA6, SCA8, SCA12, DRPLA, HD, KCNN3, and NCOA3) was analyzed in four major human groups (Africans, Europeans, Indians, and East Asians). The present analysis intends to disentangle population‐based from genetic‐based factors having shaped STR (trinucleotide) variation and to recognize, for each locus, the specific rate and pattern of mutation (bias toward expansion or contraction, constraints on allele size), and the footprints of selection. Population differences account for a very small part of the total variation, but a clear footprint appears of population growth after a bottleneck in all non‐African populations, giving support to the out‐of‐Africa model of modern humans. Most of the diversity is found among loci, and different dynamics are inferred for each of them. SCA2 and SCA3 follow an unrestricted stepwise mutation model, while the rest of loci are found under allele size constrictions and a bias to expansion (SCA1, SCA6, HD, and KCNN3), contraction (SCA12, DRPLA, and NCOA3), or unbiased (SCA8). Hum Mutat 21:61–70, 2002. © 2002 Wiley‐Liss, Inc.
Journal Article
Identification and Functional Characterization of a Novel SOX4 Mutation Predisposing to Coffin–Siris Syndromic Congenital Heart Disease
Background/Objectives: Congenital heart disease (CHD) occurs in ~1% of all live neonates globally, rendering it the most prevalent developmental anomaly affecting humans; this condition confers substantial infant morbidity and mortality worldwide. Although there is ample evidence to suggest a paramount genetic basis for CHD, the genetic etiologies underpinning the majority of CHD remain elusive. In the present study, SOX4 was selected as a significant candidate gene for human CHD, mainly because SOX4 is abundantly expressed in both human and murine hearts during embryogenesis, and the knockout of Sox4 in mice causes embryonic demise predominantly attributable to cardiovascular developmental defects. Methods: Sequencing analysis of SOX4 was fulfilled in 248 probands affected with various types of CHD and the available relatives of the identified variation carrier as well as 262 unrelated healthy individuals. Functional analysis of the mutant SOX4 protein was conducted by utilizing a dual-reporter gene system. Results: a novel heterozygous SOX4 variation, NM_003107.3:c.331G>T;p.(Glu111*), was discovered in a male proband with Coffin–Siris syndromic CHD. Genetic investigation of the proband’s available relatives revealed that the truncating variation co-segregated with the phenotype in the whole family. The nonsense variation was absent from 262 healthy controls. Functional analysis demonstrated that the Glu111*-mutant SOX4 lost transactivation on NKX2.5 and GATA4, two well-established genes that are causative factors for CHD. Moreover, the Glu111* mutation nullified the synergistic transactivation between SOX4 and TBX20, another CHD-causing gene. Conclusions: These findings support SOX4 as a causative gene accountable for familial Coffin–Siris syndromic CHD in humans. These findings may aid in developing personalized preventive and therapeutic strategies for patients with Coffin–Siris syndromic CHD.
Journal Article
DNA for Archaeologists
The ability to use DNA evidence is revolutionizing our understanding of the past. This book introduces archaeologists to the basics of DNA research so they can understand the powers and pitfalls of using DNA data in archaeological analysis and interpretation. By concentrating on the principles and applications of DNA specific to archaeology, the authors allow archaeologists to collect DNA samples properly and interpret the laboratory results with greater confidence. Written by archaeologists who conduct fieldwork as well as laboratory analysis, the volume is replete with case examples of DNA work in a variety of archaeological contexts and is an ideal teaching tool for archaeologists and their students.
eBook
Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci
Chiea Chuen Khor, Tin Aung, Francesca Pasutto, Janey Wiggs and colleagues report a global genome-wide association study of exfoliation syndrome and a fine-mapping analysis of a previously identified disease-associated locus,
LOXL1
. They identify a rare protective variant in
LOXL1
exclusive to the Japanese population and five new common variant susceptibility loci.
Exfoliation syndrome (XFS) is the most common known risk factor for secondary glaucoma and a major cause of blindness worldwide. Variants in two genes,
LOXL1
and
CACNA1A
, have previously been associated with XFS. To further elucidate the genetic basis of XFS, we collected a global sample of XFS cases to refine the association at
LOXL1
, which previously showed inconsistent results across populations, and to identify new variants associated with XFS. We identified a rare protective allele at
LOXL1
(p.Phe407, odds ratio (OR) = 25,
P
= 2.9 × 10
−14
) through deep resequencing of XFS cases and controls from nine countries. A genome-wide association study (GWAS) of XFS cases and controls from 24 countries followed by replication in 18 countries identified seven genome-wide significant loci (
P
< 5 × 10
−8
). We identified association signals at 13q12 (
POMP
), 11q23.3 (
TMEM136
), 6p21 (
AGPAT1
), 3p24 (
RBMS3
) and 5q23 (near
SEMA6A
). These findings provide biological insights into the pathology of XFS and highlight a potential role for naturally occurring rare
LOXL1
variants in disease biology.
Journal Article
Dietary Patterns and Heritability of Food Choice in a UK Female Twin Cohort
To examine the contribution of genetic factors to food choice, we determined dietary patterns from food frequency questionnaires in 3262 UK female twins aged 18 to 79 years. Five distinct dietary patterns were identified (fruit and vegetable, high alcohol, traditional English, dieting, low meat) that accounted for 22% of the total variance. These patterns are similar to those found in other singleton Western populations, and were related to body mass index, smoking status, physical activity and deprivation scores. Older subjects had higher scores on the fruit and vegetable and traditional English patterns, while lower social deprivation was associated with higher scores for fruit and vegetable, and lower scores for traditional English patterns. All 5 patterns were heritable, with estimates ranging from 41% to 48%. Among individual dietary components, a strongly heritable component was identified for garlic (46%), coffee (41%), fruit and vegetable sources (49%), and red meat (39%). Our results indicate that genetic factors have an important influence in determining food choice and dietary habits in Western populations. The relatively high heritability of specific dietary components implicates taste perception as a possible target for future genetic studies.
Journal Article
An introduction to molecular anthropology
Molecular anthropology uses molecular genetic methods to address questions and issues of anthropological interest. More specifically, molecular anthropology is concerned with genetic evidence concerning human origins, migrations, and population relationships, including related topics such as the role of recent natural selection in human population differentiation, or the impact of particular social systems on patterns of human genetic variation.
Organized into three major sections, An Introduction to Molecular Anthropology first covers the basics of genetics – what genes are, what they do, and how they do it – as well as how genes behave in populations and how evolution influences them. The following section provides an overview of the different kinds of genetic variation in humans, and how this variation is analyzed and used to make evolutionary inferences. The third section concludes with a presentation of the current state of genetic evidence for human origins, the spread of humans around the world, the role of selection and adaptation in human evolution, and the impact of culture on human genetic variation. A final, concluding chapter discusses various aspects of molecular anthropology in the genomics era, including personal ancestry testing and personal genomics.
An Introduction to Molecular Anthropology is an invaluable resource for students studying human evolution, biological anthropology, or molecular anthropology, as well as a reference for anthropologists and anyone else interested in the genetic history of humans.
eBook