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Review Doi: 10.1111/J.1469-1809.2011.00645.X Writings on Genetic Linkage in the Annals

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Review Doi: 10.1111/J.1469-1809.2011.00645.X Writings on Genetic Linkage in the Annals Review doi: 10.1111/j.1469-1809.2011.00645.x Writings on Genetic Linkage in the Annals Jurg Ott1,2 1Institute of Psychology, Chinese Academy of Sciences, 4A Datun Road, Beijing 100101, China 2Rockefeller University, New York, NY, USA Summary From its inception in 1925 through the almost 30 years that it carried the title of Annals of Eugenics, this journal published numerous articles on the statistical aspects of genetic linkage analysis and its applications to family pedigree data. This overview discusses 40 papers on linkage analysis published in the Annals. Introduction changed its name to Annals of Human Genetics. Early issues of the Annals contained various reports on family pedigree Volume I of the Annals of Eugenics was published in 1925 and data and considerations of the mode of inheritance of the was favorably reviewed in Science magazine (Holmes, 1926). trait segregating in these families. The first papers on linkage In a foreword to the first issue of the Annals, Karl Pearson, its analysis are due to Haldane (Haldane, 1934) and Fisher (Fisher, editor and the director of the Galton Laboratory for National 1934), published back to back. The two authors took issue Eugenics, and E. M. Elderton pointed out that the “develop- with the problem of estimating the recombination fraction ment of Mendelism in recent years has been in the direction when offspring cannot simply be identified as recombinants of a multiplicity of factors, even for apparently simple charac- or nonrecombinants. Haldane (Haldane, 1934) pointed out ters” (which sounds rather modern) and that “probability lies that Bernstein in the early 1930’s had recognized for the first at the basis of our knowledge.” Thus, they invited researchers time that two-generation families (without grandparents) are to publish papers (called “memoirs” at the time) on biology useful for linkage analysis and had devised a scoring system and genetics as well as mathematics and statistics. This was in relevant for such family data. Haldane then modified and stark contrast to journals issued by the Royal Society (soon improved this scoring system. Fisher applied his information to be headed by Paul Nurse, the current president of Rock- measure to these data types and demonstrated that some of efeller University (Kaiser, 2010), which is quoted as having Bernstein’s and Haldane’s formulas are not fully efficient. He issued a warning that “mathematics must not be mixed with also demonstrated how his information measure could be biology.” In fact, the publications of the Galton Laboratory applied to two parameters jointly (Fisher, 1935c). had been offered to the Royal Society Library but the offer In a pair of papers on dominant (Fisher, 1935a) and recessive was refused– a good reason for the laboratory to launch its (Fisher, 1935b) traits, Fisher proposed the use of u-scores as a own publication vehicle. more efficient way to score family data for linkage. Depending In this short review, I will outline what has been published on parental mating types, these u-scores provide simple rules in the Annals regarding linkage analysis. I found a total of for combining offspring phenotype classes into a test statistic 46 publications, mostly on methodology and a few on ap- (u-score). Fisher demonstrated that his u-scores are fully ef- plications to family data. Perhaps not surprisingly, authors ficient only for recombination fractions approaching 0.5 (no are mostly British, and male, particularly of methods papers. linkage) but are always much more efficient than Bernstein’s One outstanding female member of the Galton Laboratory y-statistics and are easy to apply. Haldane later showed that was Julia Bell. She contributed an early 15-page paper on correcting for skewness in the distribution of u-scores im- the inheritance of migraine to the Annals (Bell, 1933), but proves their statistical properties (Haldane, 1947). otherwise published mostly elsewhere (Harper, 2005). Haldane also investigated methods for detecting pseudo- autosomal linkage (then called incomplete sex-linkage) and A Quarter Century of Linkage Papers provided a list of traits such as xeroderma pigmentosum and achromatopsia that he concluded to be due to genes in This review focuses on the papers published in the Annals of the pseudo-autosomal region of the X and Y chromosomes Eugenics from its foundation in 1925 through 1954, when it (Haldane, 1936). Fisher provided further analyses of these data 344 Annals of Human Genetics (2011) 75,344–347 C 2011 The Author Annals of Human Genetics C 2011 Blackwell Publishing Ltd/University College London Genetic Linkage in the Annals by carrying out analyses of variance of u-scores, separating ef- involving nineteen traits and 903 sib-pairs” (Kloepfer, 1946), fects of linkage, and heterogeneity (Fisher, 1936b). His results and an attempt to replicate previous linkage findings con- confirmed significant evidence of linkage for some of Hal- cluded that “no signs of linkage were found between ‘strik- dane’s phenotypes. In a subsequent paper, Fisher fleshed out ingly red hair’ and the blood groups ABO, MN, P, Lewis, his approach to testing for heterogeneity by analysis of vari- Duffy, Kell and Rhesus, taste sensitivity to PTC., eye colour, ance of his u-scores and applied it to data on Friedreich’s and sex” (Hauge & Helweg-Larsen, 1954). Another publica- Ataxia but “no significant linkage could be expected from tion on allergy versus blood groups and eye color also “failed so small a group of families, especially as diagnosis must to reveal any evidence of linkage among the genes determin- have been very incomplete” (Fisher, 1936a). Together with ing these traits” (Zieve et al., 1936). In those exciting times Mather, Fisher then applied his methods to data on mice of applying the new tool of linkage analysis, it was evidently (Fisher & Mather, 1936); the authors concluded that some commonplace to report positive as well as negative linkage “suggestions of linkage ... are not conclusive but are being findings. followed up further.” At around the same time, Mather pub- Clearly, the 1930’s were a decade with many methodolog- lished a scholarly paper evaluating various family types and ical advances in linkage analysis. Leading into the 1940’s, the information they provide on linkage (Mather, 1936), and Finney published an analysis of human stature (Finney, 1939). Fisher evaluated statistical properties of the so-called product Based on linkage analysis alone, he found evidence that a formula (odds ratio) for phenotypes of offspring of inter- sex-linked gene for stature “may be present, but not giving cross matings (both parents are double heterozygotes) (Fisher, a definite conclusion.” When he took into account parental 1939). statures, he observed strong correlations between parents and Penrose (Penrose, 1935) came up with the revolutionary offspring but no evidence for linkage. The author concluded idea that even a single generation of individuals can be used that “in view of the various seeming contradictions found to test for linkage. He considered two phenotypes (presum- in the data, it would be undesirable to place trust in any re- ably under some form of genetic control), each with two sults derived therefrom without first testing them on other levels of expression. This allows the representation of sib-pair records” (Finney, 1939). This analysis reminds me of a re- data in four classes displayed in a 2 × 2 table. Penrose showed cent population-based study showing that a genomic profile that in the presence of linkage the two classes, in which sib- of 54 loci explains only ∼5% of the variance of stature but pairs are either both alike or both unlike with respect to the mid-parent values explains 40% of the variance (Aulchenko two phenotypes, will occur in higher frequencies than ex- et al., 2009). Building upon Fisher’s previous work, Finney pected by chance. He demonstrated his new method on the then went on to publish a series of papers on the detection basis of 60 sib-pairs scored for red hair, blue eyes, and A of linkage allowing for incompleteness of parental genotyping and B agglutinogens. He concluded that linkage may exist and for combining data from matings of known and unknown for genes influencing red hair and agglutinogen. Penrose later phase (Finney,1940, 1941a, b, 1942a, b, 1943). Also in the mid extended his method to the analysis of quantitative traits (Pen- 1940’s, Kosambi published his well-known recipe on con- rose, 1938) and applied improvements of it (Penrose, 1946, verting recombination fractions into map distances (Kosambi, 1953) to the phenotypes red hair versus ABO blood types 1944). (Penrose, 1950) and phenylketonuria versus ABO and MN On the basis of 17 pedigrees segregating color blindness blood types (Penrose, 1951). While the latter investigation and hemophilia, two X-linked genes previously known to be furnished inconclusive results, results for red hair versus ABO linked, Haldane and Smith undertook a thorough analysis of seemed “highly unlikely to be a chance variation” (Penrose, the data employing several methods including that of max- 1950). imum likelihood (Haldane & Smith, 1947). They found a The simplicity of the sib-pair test for linkage led to a flurry maximum likelihood estimate of the recombination fraction of publications on all kinds of linkage investigations. In the of 9.8%. This is an interesting paper, even today, as it demon- Annals, 500 pairs of sibs were scored for such phenotypes as strates how linkage analysis by maximum likelihood may be presence of hair in the mid-digital regions of the fingers, abil- carried out. ity to taste phenyl-thiocarbamide (PTC), and various blood Towards the late 1940’s and early 1950’s, several method- types (Boyd & Boyd, 1941). The authors of this investigation ological papers addressed varying aspects of linkage analysis.
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