MHC Genomics and Disease: Looking Back to Go Forward

Ancestral haplotypes are conserved but extremely polymorphic kilobase sequences, which have been faithfully inherited over at least hundreds of generations in spite of migration and admixture. They carry susceptibility and resistance to diverse diseases, including deficiencies of CYP21 hydroxylase (47.1) and complement components (18.1), as well as numerous autoimmune diseases (8.1). The haplotypes are detected by segregation within ethnic groups rather than by SNPs and GWAS. Susceptibility to some other diseases is carried by specific alleles shared by multiple ancestral haplotypes, e.g., ankylosing spondylitis and narcolepsy. The difference between these two types of association may explain the disappointment with many GWAS. Here we propose a pathway for combining the two different approaches. SNP typing is most useful after the conserved ancestral haplotypes have been defined by other methods.

Haplotypes for Type, Degree, and Rate of Marbling in Cattle Are Syntenic with Human Muscular Dystrophy

Traditional analyses of a QTL on Bota 19 implicate a surfeit of candidates, but each is of marginal significance in explaining the deposition of healthy, low melting temperature fat within marbled muscle of Wagyu cattle. As an alternative approach, we have used genomic, multigenerational segregation to identify 14 conserved, ancestral 20 Mb haplotypes. These determine the degree and rate of marbling in Wagyu and other breeds of cattle. The melting temperature of intramuscular fat is highly heritable and traceable by haplotyping. Fortunately, for the production of healthy beef, some of these haplotypes are sufficiently penetrant to be expressed in heterozygous crossbreds, thereby allowing selection of sires which will improve the healthiness of beef produced under even harsh climatic conditions. The region of Bota 19 is syntenic to a region of Hosa 17 known to be important in muscle metabolism and in determining susceptibility to a form of human muscular dystrophy.

Soma-to-germline feedback is implied by the extreme polymorphism at IGHV relative to MHC: The manifest polymorphism of the MHC appears greatly exceeded at Immunoglobulin loci, suggesting antigen-selected somatic V mutants penetrate Weismann's Barrier

Soma-to-germline feedback is forbidden under the neo-Darwinian paradigm. Nevertheless, there is a growing realization it occurs frequently in immunoglobulin (Ig) variable (V) region genes. This is a surprising development. It arises from a most unlikely source in light of the exposure of co-author EJS to the haplotype data of RL Dawkins and others on the polymorphism of the Major Histocompatibility Complex, which is generally assumed to be the most polymorphic region in the genome (spanning ∼4 Mb). The comparison between the magnitude of MHC polymorphism with estimates for the human heavy chain immunoglobulin V locus (spanning ∼1 Mb), suggests IGHV could be many orders of magnitude more polymorphic than the MHC. This conclusion needs airing in the literature as it implies generational churn and soma-to-germline gene feedback. Pedigree-based experimental strategies to resolve the IGHV issue are outlined.

A novel method of measuring the melting point of animal fats

The melting point (TM) of fat is relevant to health, but available methods of determining TM are cumbersome. One of the standard methods of measuring TM for animal and vegetable fats is the slip point, also known as the open capillary method. This method is imprecise and not amenable to automation or mass testing. We have developed a technique for measuring TM of animal fat using the Rotor-Gene Q (Qiagen, Hilden, Germany). The assay has an intra-assay SD of 0.08°C. A single operator can extract and assay up to 250 samples of animal fat in 24 h, including the time to extract the fat from the adipose tissue. This technique will improve the quality of research into genetic and environmental contributions to fat composition of meat.

The effects of automated encoders on coding accuracy and coding speed

Encoded data on diagnoses and procedures are put to a broad range of uses. Coding accuracy and speed are imperative. One method that coding experts have recommended to improve coding accuracy and speed is automated encoders. The article describes the effect of automated encoders on coding accuracy and speed when used by trained coding staff. A study involving six Veterans Administration medical centers found that, overall, coding accuracy improved 19.4 percent after implementation of encoding software. The effect on coding speed, however, depended on the system set-up, with some set-ups actually reducing the number of discharges coded per day.

Free radicals and septic shock in primates: the role of tumor necrosis factor

The role of free radicals in septic-shock-associated tissue injury and the mechanisms underlying the generation of free radicals in sepsis was investigated in a primate model using electron spin resonance (ESR) spectroscopy and spin-trapping techniques paired with physiological measurements. Baboons were administered the spin trap, 5,5-dimethyl-1-pyrroline N-oxide (DMPO) during infusions of live Escherichia coli (E. coli) with or without challenge with tumor necrosis factor (TNF). ESR spectra suggesting the trapping of carbon-centered and oxygen-centered radicals were detected in liver lipid extracts of E. coli infused animals which exhibited pathophysiological changes indicative of sepsis. In animals demonstrating a toxic response to E. coli. TNF challenge appeared to intensify the ESR signal observed. These data provide evidence of free radical production during sepsis and suggest a role for TNF in the production of these radicals.

Automated information systems provide health information management support to veterans' healthcare

The Veterans Health Administration has implemented a comprehsnsive DHCP which supports the VA healthcare system at both local and national levels. Numerous clinical and management modules have been developed; an overview was given of selected applications impacting health information managers. Continuing development includes an automated clinical record and expanded electronic data exchange.

Physician and coding errors in patient records

The Veterans Administration's discharge abstract system was studied to identify error frequency, source, and effect in five Veterans Administration hospitals. We reviewed 1,829 medical records from 21 services for concordance with the abstract; sampling provided 95% confidence for each service. Of these records, 1,499 (82%) differed from the abstract in at least one item. Of 20,260 items, 4,360 (22%) were incorrect, with three error sources: physician (62%), coding (35%), and keypunch (3%). We projected 2.14 physician and 0.81 coding errors in the average abstract. Eighty-nine percent of projected physician errors were failures to report a procedure or diagnosis. Coding was subjective and errors were synergistic with physician errors. We projected that correction of errors would change 19% of the records for diagnosis-related group purposes and substantially increase future resource allocation. This effect varied considerably by service.