SPECIAL FEATURES

MEETING ANNOUNCEMENTS

March 24-28, 1991-Mathematical Analysis of the Hu- man Genome: DNA Sequence to Protein Structure

Santa Fe, New Mexico Telephone: 415-486-4943 (Fax: 415-486-5717)

April 21-27, 1991-International School of Medical Ge- netics (Fourth Annual Course)

Grignano (Trieste), Italy (First three courses in Sestri Levante) Telephone: 39-lo-56.36-370/400 (Fax: 39-10-56-36-461)

May 8-12,1991-Genome Mapping and Sequencing III Cold Spring Harbor Laboratories, New York Telephone: 516-367-8346 (Fax: 516-367-8845)

June 2-4,1991-Human Genome Research in an Interde- pendent World: International Aspects of Ethical, Legal, and Social Issues

(By invitation only) Washington, D.C. Telephone: 608-263-3414 (Fax: 608-262-2327)

July 13-16, lSSl-Annual Meeting, European Society of Human Genetics

Leuven, Belgium Telephone: 32-16-21-58-60 (Fax: 32-16-21-59-97)

July 22-August 2, 1991-32nd Annual Short Course in Medical and Experimental Mammalian Genetics

Bar Harbor, Maine Telephone: 207-288-3371 (Fax: 207-288-5079)

August 18-12, 1991-Human Gene Mapping 11 (HGMll)

London, United Kingdom Telephone: 44-71-269-3052 (Fax: 44-71-430-1787)

September 22-25, 1991-DNA Sequencing III Hilton Head, South Carolina Telephone 301-480-0634 (Fax: 301-480-8588)

October 6-11, 1991-Eighth International Congress of Human Genetics

Washington, D.C. Telephone: 301-571-1825 (Fax: 301-530-7079) (See detailed notice in this issue)

October 2 l-23-Human Genome III: International Confer- ence on the St,atus and Future of Human Genome Re- search

(Sponsored jointly by Science magazine and HUGO) San Diego, California Telephone: 212-730-1050 (Fax: 212-382-1921)

MEETING REPORT

Guidelines for Human Linkage Maps: An International System for Human Linkage Maps (ELM, 1990)

BRONYA J. B. KEATS,’ STEPHANIE L. SHERMAN,’ NEWTON E. MORTON,~ ELIZABETH B. ROBSON,~ KENNETH H. BUETOW,~ PETER E. CARTWRIGHT,~ ARAVINDA CHAKRAVARTI,~ UTA FRANCKE,~ PHILIP P. GREEN,~ AND JURG OTT”

‘Department of Biometry and Genetics, LouIslana State University Medical Center, New Orleans, Louisiana 70112; ‘Division of Medical Genetics, Emory University, Atlanta, Georgia 30302; 3Department of Community Medicine, University of Southampton, Southampton SO9 4XY, United Kingdom; 4The Galton Laboratory, University College London, London NW1 ZHE, United Kingdom; ‘Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111; 6Howard Hughes Medical Institute, University of Utah Medical Center, Salt Lake City, Utah 84132; ‘Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania 15261; ‘Department of Genetics and Howard Hughes R/led/Cal Institute, Stanford University Medical Center, Stanford, California 94305; ‘Department of Genetics, Washington University School of Medicine, St. Lou& Missouri 63 7 7 0; and “Department of Psychiatry, Columbia University, New York, New York 10032

Maps of the human chromosomes include linkage maps derived from meiotic recombination rates and measured in centimorgans (CM) and physical maps based on a variety of experimental approaches. They should agree in order but not necessarily in relative distances between loci. Gene mapping subsumes all of these maps. Here we are con- cerned primarily with the linkage map, which is often called the “genetic map.”

For most human chromosomes, several linkage maps have now been published. They dialer in many respects, including position of the origin, choice of locus names, mea- sures of statistical support for locus order, level of interfer- ence, allowance of sex differences and data errors, and incor- poration of other mapping information. Therefore, a sys- tem of standards for the construction and representation of linkage maps has become necessary. Such standardization will lead to an understanding of the relation between link- age and physical maps, allow more reliable risk estimates for genetic counseling, and contribute to the international human genome mapping and sequencing efforts. Standard- ization has been achieved for nomenclature of gene loci (ISGN, 1987) and chromosome bands (ISCN, 1978, 1981)

GENOMICS 9, 557-560 557 08X8-X54:3/91 $3.00 Copyright IL’ 1991 hy Academic Press. Inc.

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SPECIAL FEA TURES

and has proven beneficial to human genetics. In this tradi- tion a meeting was organized at Bethesda, Maryland, in ,June 1990, and the following guidelines for the presentation

and standardization of linkage maps were drawn up by the participants.

General Standards

I~cs&~natiorz c$ loci. Locus symbols for genes and anony- mous DNA segments are standardized by international committees that report to Human Gene Mapping Work- shops (HGMW). Therefore, maps should use these

HGMW-approved symbols for assigned loci. Provisional symbols for newly identified gene loci should he reported to the Nomenclature Committee* (McAlpine et nl.. 1989). In formation regarding probes for anonymous DNA segments should he referred to the DNA Committee (Kidd et (I!..

1989). Descriptive attributes of a locus. including name, symbol, class (e.g., disease, isozyme, RFLP. (dC-dA),(dG dT), microsatellite, minisatellite or VNTR. et,c.), prohe name, PCR primers, allele frequencies. heterozygosity, and penetrance. should he referenced and/or tahulat,ed. The

practice of referring to loci hy probe names, arhitrary num- hers, and other nanstandard symbols on maps should be avoided.

Framc~rcvrk loci. 120ci for which order on a linkage map is well supported are termed frame-work loci; a map composed entirely of such loci is called a framwwrk ~nnp. Such maps are reliahle, although their resolution may he low. Frame-

work loci merit tirst consideration fnr precise physical as- signment and development into sequence tagged sites (ST%; Olson pt al., 1989). In addition, every etfort should he made to deposit prohes for framework loci into an appro- priate repository for public access.

A map is called comprcl2c~nsicrt, if it aims to include all syntenic loci. Comprehensive maps are dense but may be locally unreliable with respect to both order and distance. Map intervals in a comprehensive map are delimited hv

framework loci. Investigators should identify the framework loci in their

maps. Chromosome committees may review such loci to es-

tablish a working set of framework loci for general use. This will facilitate integration of’ linkage maps. Criteria for choosing such loci may include level of het,erozygosity and availahility of probes or sequence data. The working set of loci may he updated hy substitutions and additions as new

framework loci are identified. Other terms that have been proposed to specify sets of

loci with particular attrihutes include arbitrary reference points (ARPs; Kidd et al.. 1989) and index loci (Roberts, 1990). They may overlap with framework loci. hut are de- fined ditferently. ARPs are markers with precise physical locations that are scaled by arm length to give order with-

* To obtain information en the assignment of symt)ols fbr new]\ identilied gene loci and Wnumhers t’or anonymous DNA sex merits. contact the (:enome Data Hase hv telephone at 301-R% WU or hy Fax at :Wl-955-0051.

out physical distance. Index loci are highly polymorphic and are 10 to 15 cM apart.

Support. Hierarchical types of support, all based on the common logarithm of a likelihood ratio. log,,,(L,/L,). have heen defined. They are global support, intczrrwl support. and

support for order. Clnhal support is detined as the evidence that. a marker

helongs to a linkage group. It is expressed as a lad score which is calculated hy taking L, as the maximum likelihood

when the marker is inserted in the map and L, as the likeli- hood when the marker has free recombination with the map. A claim of linkage based on genetic evidence requires global support of’ at least 3. corresponding to odds of 1OOO:l. This is a minimal standard, appropriate for a single marker

with only a single parameter (the recombination fraction) estimated.

Interval support is defined as the evidenc,e that a marker is in a specified order relative to the framework loci. In this case, I,, is the likelihood under the given order and lJ2 is the highest likelihood obtained hy interchanging the marker

with the flanking framework loci or 1)y placing it in any other interval on the framework map. When the level ot interval support exceeds :3. the marker should he designated a framework locus. Alt bough this value may he cnnserva- tive hased on statistical theory, empirical evidence suggests

that it may he necessarv hecause of the etiects of lahnratory errors, degree of map resolution. number of’ loci. and meth- ods of analysis. Experience and empirical observations will determine if this value is appropriate.

Support for order of a set of loci is given by log,,,(L,/L,), where L,, is the likelihood under the favored order and L,

-Z L, is the likelihood under a competing order. It. is recom- mended that the ratio he at least 3 for the framework map versus the next best order.

f kirnlntion of Mnps. By convention, the Human (;ene Mapping Workshop Committee Reports list loci assigned

to chromosome hands in the order pier to qter. The order of loci is identical for physical and linkage maps and thus loci on a linkage map should he given in the order pter yter. so that any contradiction between physical assignment and

linkage map order is readily apparent. SPX differvncc.5. Male and female maps should he esti-

mated separately. constrained hy order. In situations where this is not possible due to limited data, a ratio. fi. of map intervals for the two sexes may he estimated as 111, &I,,

where u:r and u’,,, are map distances in females and males, respectively. However, extensive data over a large interval often rqject this model. Available data have suggested that there is an excess of female recombination near the centro-

mere and an excess of male rec,omhinatinn near the telo- meres, conforming to the observation that chiasmata are more localized in the sex with the shorter map (Haldane. 1922). However. this relation is not known precisely and thus its mathematical form cannot lie specified as yet. I,o- tally, large sex ditferences occur in humans and they can have substantial efl’ects on genetic predict ion.

I [nits of mcnsurcmc~nt and intwfcrcnc.~~. Linkage map dis- tances should he measured in centimorgans. with the level

of interference assumed in an analysis clearly specified. The recombination fraction, 0, may be expressed in terms of the map distance in Morgans, ID, and a level of interference.

At the limit of complete interference, B = LLI. At the limit of null interference, H = (1 - em2”)/2. The classical mapping functions used in human linkage analysis include those of Carter and Falconer (1951), Kosambi (1944), and Haldane (1919). Rao et al. (1977) derived a mapping function in terms of an interference parameter, p, that includes all of

these as special cases. The value ofp = 0.35 has been esti- mated (Morton et al., 1977), and there is evidence that it may be appropriate for human data (Morton and Collins, 1990). Most multipoint linkage analyses performed to date estimate recombination fractions under the unrealistic, but

simplifying, assumption of null interference. Misidt~ntific.atior2, misclassification, and duplication

errors. Errors of identification include misstatement of par- entage, errors in recording identifying information, and in- terchange of samples. These errors may occur at the time of

collection, during processing in the laboratory, or when re- sults are entered for linkage analysis. Many, but not all, of these errors are detected as parentage exclusions. Reasons for misclassification of phenotypes include contamination

and degradation of samples, misplacement in a set of sam- ples, misinterpretation of bands or reactions, and errors in recording data. The most reliable control for such errors is obtained by duplicate typing of all loci, blind to family rela- tionships and previous results. A cheaper alternative is to retest all apparent recombinants over small distances and

all double recombinants over moderate distances. Unfortu- nately, duplicate typing is not done routinely, and only a proportion of critical results are retyped. Therefore many errors go undetected. These errors affect both order and estimates of distance.

In a sequence ABC, the effect of an undetected typing error at locus B is to simulate double recombination be-

tween the flanking markers A and C. A recent comparison of duplicate typings from different laboratories found a dis- cordance frequency of about I”;, corresponding to an ap- proximate error rate of 0.5% (White et al., 1990). Morton and Collins ( 1990) e&mated that an error rate as small as 0.5% could infiate t.he length of a map of 100 loci by as

much as 100 CM. A simulation study of family structures consisting of grandparents, parents, and offspring (Jiang and Buetow, 1990) found that with a 1.5od error rate and five loci on the map the average interlocus distance in- creased from 1.8 to 4.7 CM. In addition, their analysis showed that 3.4”;~ of orders for which support for order was greater than 3 were incorrect. Another simulation study (Terwilliger et (zl., 1990) analyzed two loci with three alleles each and showed that. an overall (both detected and unde- tected) error rate in marker typing of 5% increased the re- combination rate from 2 to 7°C and decreased the expected

lod score bv nearly 25’0. Clearly, hyping errors should be kept to a minimum and

routine duplicate typing is strongly recommended. If the frequency ol’tyl,ing errors is approximately known, then it

may be taken into account iI1 he i: L agt ; (1; I?<,> (~ 11. 1985). This tends to elimirate tile h a; ir hta e+li[l,:~ erl

map distances and it reduce; IL: 9 :)r )l:s’,ili v ot sllrtria)u;l,. high levels of support for inc*jrr.r ‘t old r+. A[, Itl:er INFIX 111, method of approximately adj u: tin;: ti II ! pit g:‘r!o~s no (v III’

to scale interval distances ai’c,jr iin? 11, the t’.iirll; tell II :,,I length.

Errors in linkage maps a(‘e a so (a:ised ‘1: ir C~USI(III ot overlapping data in t.he anal!~s s. ‘I’h,, I rzcise dent ific.;ltiorl of families included in a link:.glJ stud!. i:, e,rit .c.11 t’;)r arc.!lil:al

purposes and combination \vi b other clat:.. In\~e+tig:lror~ are urged lo make sure that thty UII~ 1 higuclus:y identll\- the families in their study b!, c ti- tinp t 141 SOLII ce. pro\ iding pedigree identification numl)ers. an 3 ,:cplairhing in detail

any overlap with published an:llJ,scs. In adtlition. il an!’ part of the pedigree structure is altel,ecl rn h 1 ublication to ensure confidentiality, this s1c1u.d bt stated c iearl:\..

Auailabilit~, and nccessibilit)~ ot link aA 6’ data and n2op.s. It is strongly recommended that ~‘aw pherotype lata oe avail- able on request and that pairwise lad sI:ores be deposited into a database for easy accessibility t(l i he SC ientific com-

munity.

Unresolved lssu :s

Whereas the guidelines were unar inlous, there was dis-

agreement about several impc’rtant is:iues. They are out- lined in this last section as mai ters to t le resolved at a later time.

Origin of the map. Two alternatives for the origin of the map were suggested: the telomel~e of the short arm (pter)

and the centromere. Advocates for the placctment of the origin at the telomere stated that starting at ;,ter makes it easy to sort on location, simplif& calculation of distance, and avoids negative number:i and/o). prefixe:; (p or y). In addition, maps of all other cNrganisn,s begin .-it one of the telomeres. Arguments for positioning the orig.n at the cen-

tromere included the convention t lat both cytogenetic bands and ARPs are numbered from the centromere, cen- tromeric markers are currently availab e for most chromo- somes whereas fewer telomeric rnarLel,s are \,et available, and centromeric mapping using ovarian teratomas sets a precedent for the centromere as an origin for genetic maps.

A third group preferred not to specify ;m origin and to repre- sent a map by interval distances. Ad&t ion is then required to determine distances bet.ween nonadj:Jcent l~~ci.

Presentation of location data. Sum nary maps should be ordered by linkage and physical data. T’iere was agreement

that the minimal dat,a set to describe a locus should include cytogenetic assignment, genetic location for each sex in cM, the two flanking framework loci (interval1 assignment), and whether or not it is a framework locu:;. However, there was disagreement about how 1ocatic)n shouid be specified, and the most useful way to order loci by li;7kage and physical data simultaneously.

Methodological issues. It was recogmzed that methodoloy- ical issues could not be resolved at this meeting but should

559

SPECIAL FEATURES

be addressed on another occasion. Such issues include the strategy for constructing a map and the presentation of the subset of orders considered in the analysis.

ACKNOWLEDGMENTS

This workshop was supported by the l1.S. Public Health Service Research Grant HG 00231 from the National Center for Human Genome Research, and the Medical Research Council of Great Britain.

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REFERENCES

CARTER, T. C.. AND FALCONER. D. S. (1951). Stocks for de- tecting linkage in the mouse and the theory of their design. J. Genet. 50: 307-323.

HALDANE, J. B. S. (1919). The combination of linkage values and calculation of distance between the loci of linked factors. J. Genrt. 8: 299-309.

HALDANE, .J. B. S. (1922). Sex ratio and unisexual sterility in hybrid animals. J. &net. 12: 101-I 09.

HEALY, M. ,I., AND WHITEHEAD, T. 1’. (1980). Outlying values in the National Quality Control Scheme. Ann. Clin. Riochem. 17: Z-81.

ISCN 1978 (1978). An international system for human cytoge- netic nomenclature. CUytogencr. (‘c/l Genrt. 21: 303-404.

ISCN 1981 (1981). An international system for human cytoge- netic nomenclature: High resolution banding. C’ytoEenet. C’el( Genet. 31: l-23. ISGN 1987 (1987). Guidelines for human gene nomenclature: An international system for human gene nomenclature (ISGN, 1987). Cytogenet. Cell &net. 46: 11&28.

,JIANG, 0. X., AND BUETOW, Ii. H. (1990). Simulation evalua- tion of high resolution meiotic gene mapping. (Abstract). Am. J. Hum. Genet.. in press.

KIDD, K. K., BOWCOCK, A. M., QCHMIDTKE, J., TRACK, R. K.. RIC.CIUTI, F., HUTCHINGS, G., BAI.E, A.. PEARSON, P., AND

WILLARD. H. F. (1989). Report of the DNA committee and catalogs of cloned and mapped genes and DNA polymor- phisms. Cvtogwzet. CeII Genet. 51: 622-947.

KOSAMBI, 1). D. (1944). The estimation of map distances from recombination values. Ann. b’ugenet. 12: 172-175.

MCALPINE. P. -1.. SHOWS, T. B.. BO~JCHEIX. ‘Z.: STRANC, L. C.. BERENT, T. B., PAKSTIS, A. J., AND DOUTE, R. C’. (1989). Report of the nomenclature committee and the 1989 catalog of mapped genes. Clvtogenet. Cell Cknet. 51: 13-66.

MORTON, N. E., AND COLLINS, A. (1990). Standard maps of chromosome 10. Ann. Hum. &net.. in press.

MORTON, N. E., LINDSTEN, .J.. ISELIUS, L.. AND YEE. S. (1982). Data and theory for a revised chiasma map of man. Hum. (knei. 62: 266-270.

MORTON, N. E., RAO, D. C., LINDSTEN, J., HULTEN. M.. AND

YEE, S. (1977). A chiasma map of man. Hum. Herrd. 27: 3% 51.

OLSON, M., HOOD, L., CANTOR, C., AND BOTS’FEIN, D. (1989).

A common language for physical mapping of t.he human ge- nome. Science 245: 1434-1435.

OTT, .J. (1985). “Analysis of Human (ienetic Linkage.” Johns Hopkins IJniv. Press, Baltimore.

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RAO, D. C., MORTON, N. E., LINDSTEN, .J., HULTEN, M., AND YEE, S. (1977). A mapping function in man. Hum. Hered. 27: 99-104.

ROBERTS, L. (1990). The genetic map is back on track aft.er delays. Science 248: 805.

TERWILLIGER, .J. D.. WEEKS, D. E., AND OTT, J. ( 1990). Over- estimation of the recombination fraction and loss of informa- tion due to typing errors. (Abstract). Am. J. Hum. Genet., in press. WHITE, R. L., LALOUEL, .I.-M., NAKAMU~ZA, Y., DONIS-

KELLER, H., GREEN. P.. BOWDEN, D. W., MATHEW, (1. (:. I’., EASTON, D. F., ROBSON, E. B., MORTON, N. E., GUSELLA,

J. F., HAINES, ,J. L., RETIEF, A. E., KIDD, K. K., MURRAY, .J. C., J>ATHROP, G. M., AND CANN, H. M. (1990). The CEPH consortium primary linkage map of human chromosome 10. (bwmics 6: 393-412.

MEETING REPORT

A New European Effort- Techniques That Analyze Complex Genomes (TACpG)

DAVID GRAUSZ

Laboratoire d’tiematologie Experimentale, UPR 47 CNRS, H6pital St. Louis, 1 av. Claude Vellefaux, 75475 Paris C&dex 70, France

The 24th INSERM workshop at Le Hohwald, March 21& 24, 1990, assembled European scientists (Table 1) using techniques that analyze complex genomes (TACpG). It set out to establish the state-of-the-art in pulsed-field gel elec- trophoresis (PFGE), YAC cloning, contig mapping, jump- ing, linking, and the physical manipulation of chromo- somes (sorting and micromanipulation).

The Mapping Specialist Is Faced with a Series of Crucial @estions

There has been much discussion concerning the relative merits of physical versus genetic linkage mapping tech- niques. The genetic linkage approach allows a picture of the entire genome, complete to the extent that polymorphic loci are available (especially with microsatellite sequences that seem ubiquitous in the genomes of species from yeast to man). In contrast, the physical mapper, whether using a semistatistical or more directed approach (e.g., fragile X), aims to cover 95-98s of the region, chromosome, or ge- nome in question with cosmid and/or YAC contigs.

What is the significance of that last 2 to 5% which is almost impossible to clone? Is there a global strategy that can be followed to disclose its nature? PCR clearly offers

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