THE DESIGN AND ANALYSIS OF EXPERIMENTS. By Oscar Kempthorne. New York, John Wiley and Sons, Inc., 1952. 631 pp. $8.50. This book by a teacher of statistics (as well as a consultant for \"experimenters\") is a comprehensive study of the philosophical background for the statistical design of experiment. It is necessary to have some facility with algebraic notation and manipulation to be able to use the volume intelligently. The problems are presented from the theoretical point of view, without such practical examples as would be helpful for those not acquainted with mathematics. The mathematical justification for the techniques is given. As a somewhat advanced treatment of the design and analysis of experiments, this volume will be interesting and helpful for many who approach statistics theoretically as well as practically. With emphasis on the \"why,\" and with description given broadly, the author relates the subject matter to the general theory of statistics and to the general problem of experimental inference. MARGARET J. ROBERTSON

The Design and Analysis of Experiments

This report updates the 2002 recommendations by the Advisory Committee on Immunization Practices (ACIP) on the use of influenza vaccine and antiviral agents (CDC. Prevention and Control of Influenza: Recommendations of the Advisory Committee on Immunization Practices [ACIP]. MMWR 2002;51 [No. RR-3]:1-31). The 2003 recommendations include new or updated information regarding 1) the timing of influenza vaccination by age and risk group; 2) influenza vaccine for children aged 6-23 months; 3) the 2003-2004 trivalent inactivated vaccine virus strains: A/Moscow/10/99 (H3N2)-like, A/New Caledonia/20/99 (H1N1)-like, and B/Hong Kong/330/2001-like antigens (for the A/Moscow/10/99 [H3N2]-like antigen, manufacturers will use the antigenically equivalent A/Panama/2007/99 [H3N2] virus, and for the B/Hong Kong/330/2001-like antigen, manufacturers will use either B/Hong Kong/330/2001 or the antigenically equivalent B/Hong Kong/1434/2002); 4) availability of certain influenza vaccine doses with reduced thimerosal content, including single 0.25 mL-dose syringes; and 5) manufacturers of influenza vaccine for the U.S. market. Although the optimal time to vaccinate against influenza is October and November, vaccination in December and later continues to be strongly recommended A link to this report and other information regarding influenza can be accessed at http://www.cdc.gov/ncidod/diseases/flu/fluvirus.htm.

https://stacks.cdc.gov/view/cdc/6625/cdc_6625_DS1.pdf

Prevention and control of influenza : recommendations of the Advisory Committee on Immunization Practices (ACIP)

Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty.

Results: We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors.

Availability: http://samtools.sourceforge.net 

Contact: hengli@broadinstitute.org

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

Age-related macular degeneration (AMD) is a major cause of blindness in the elderly. We report a genome-wide screen of 96 cases and 50 controls for polymorphisms associated with AMD. Among 116,204 single-nucleotide polymorphisms genotyped, an intronic and common variant in the complement factor H gene ( CFH ) is strongly associated with AMD (nominal P value -7 ). In individuals homozygous for the risk allele, the likelihood of AMD is increased by a factor of 7.4 (95% confidence interval 2.9 to 19). Resequencing revealed a polymorphism in linkage disequilibrium with the risk allele representing a tyrosine-histidine change at amino acid 402. This polymorphism is in a region of CFH that binds heparin and C-reactive protein. The CFH gene is located on chromosome 1 in a region repeatedly linked to AMD in family-based studies.

/pdf/complement-factor-h-polymorphism-in-age-related-macular-1je6ex4sfb.pdf

Complement Factor H Polymorphism in Age-Related Macular Degeneration

Genetic factors strongly affect susceptibility to common diseases and also influence disease-related quantitative traits. Identifying the relevant genes has been difficult, in part because each causal gene only makes a small contribution to overall heritability. Genetic association studies offer a potentially powerful approach for mapping causal genes with modest effects, but are limited because only a small number of genes can be studied at a time. Genome-wide association studies will soon become possible, and could open new frontiers in our understanding and treatment of disease. However, the execution and analysis of such studies will require great care.

Genome-wide association studies for common diseases and complex traits

A key step toward the discovery of a gene related to a trait is the finding of an association between the trait and one or more haplotypes. Haplotype analyses can also provide critical information regarding the function of a gene; however, when unrelated subjects are sampled, haplotypes are often ambiguous because of unknown linkage phase of the measured sites along a chromosome. A popular method of accounting for this ambiguity in case-control studies uses a likelihood that depends on haplotype frequencies, so that the haplotype frequencies can be compared between the cases and controls; however, this traditional method is limited to a binary trait (case vs. control), and it does not provide a method of testing the statistical significance of specific haplotypes. To address these limitations, we developed new methods of testing the statistical association between haplotypes and a wide variety of traits, including binary, ordinal, and quantitative traits. Our methods allow adjustment for nongenetic covariates, which may be critical when analyzing genetically complex traits. Furthermore, our methods provide several different global tests for association, as well as haplotype-specific tests, which give a meaningful advantage in attempts to understand the roles of many different haplotypes. The statistics can be computed rapidly, making it feasible to evaluate the associations between many haplotypes and a trait. To illustrate the use of our new methods, they are applied to a study of the association of haplotypes (composed of genes from the human-leukocyte-antigen complex) with humoral immune response to measles vaccination. Limited simulations are also presented to demonstrate the validity of our methods, as well as to provide guidelines on how our methods could be used.

Score Tests for Association between Traits and Haplotypes when Linkage Phase Is Ambiguous

https://www.immunize.org/laws/influenza_for_healthcare_workers.pdf

Requiring influenza vaccination for health care workers: seven truths we must accept

Background
Immunization rates for children and adults are rising, but coverage levels have not reached optimal goals. As a result, vaccine‐preventable diseases still occur. In an era of increasing complexity of immunization schedules, rising expectations about the performance of primary care, and large demands on primary care providers, it is important to understand and promote interventions that work in primary care settings to increase immunization coverage. One common theme across immunization programs in many nations involves the challenge of implementing a population‐based approach and identifying all eligible recipients, for example the children who should receive the measles vaccine. However, this issue is gradually being addressed through the availability of immunization registries and electronic health records. A second common theme is identifying the best strategies to promote high vaccination rates. Three types of strategies have been studied: (1) patient‐oriented interventions, such as patient reminder or recall, (2) provider interventions, and (3) system interventions, such as school laws. One of the most prominent intervention strategies, and perhaps best studied, involves patient reminder or recall systems. This is an update of a previously published review.

/pdf/patient-reminder-and-recall-interventions-to-improve-3ug3aafnfb.pdf

Patient reminder and recall interventions to improve immunization rates

Today, the most recent in a long line of antivaccinationists are using modern media to sway public opinion and distract attention from scientific evidence. But there are steps we can take to avert the ill effects of these campaigns.

The Age-Old Struggle against the Antivaccinationists

A 25-year-old registered nurse comes for a visit to initiate prenatal care after receiving a positive result on a pregnancy test. On review of her vaccination status, she reports that she declined hepatitis B vaccination when it was offered by her current employer because she does not draw blood and thus does not consider herself at risk. Should she receive the vaccine? What are the current recommendations for hepatitis B vaccination?

Robert M. Jacobson

Papers

Score Tests for Association between Traits and Haplotypes when Linkage Phase Is Ambiguous

Requiring influenza vaccination for health care workers: seven truths we must accept

Patient reminder and recall interventions to improve immunization rates

The Age-Old Struggle against the Antivaccinationists

Prevention of Hepatitis B with the Hepatitis B Vaccine