Report of the fifth international workshop on human X chromosome mapping Page: 2 of 33
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indispensible. Several approaches were proposed to satisfy the
general needs. In addition to the extension of individual
integrated reference activities (such as the Lehrach group at
ICRF), several groups, starting with the Human Genome
Centers at Washington University and Baylor College of
Medicine and the Leiden group, have agreed to deposit sets of
X-specific YACs at the American Type Culture Collection
repository (Rockville, MD, USA). The ATCC repository
would provide materials at nominal cost (per clone or per
collection) in a manner analogous to its handling of lambda
clones or bacterial plasmids in the past. With appropriate
references to the literature and links to databases, this could
give everyone an entree to useful current clones. The
discussions acknowledged, however, that clones are transient,
since "better" ones will become available with improvements in
cloning technology, and new developments like long-range
PCR could greatly change the entire way in which a map is
stored and recovered, sharply reducing the dependence on
stored banks of clones.
The definition of a finished map and its quality received
some discussion in pointing toward the next phase of mapping
efforts. -The definition accepted for map completion by the
U.S. NIH (100 kb resolution with ordered STSs and up to
100% continuity) is a demanding one, but offers a standard
with markers stationed on average near every second or third
gene, and near enough to permit easy recovery of new cognate
clones of various types. Regions like portions of Xp22 (abs. 2
and 6), Xpl1.21 (abs. 82) and most of Xq24-qter (abs. 54)
already show that this standard can be achieved; and the
Washington University Center reported a census of 1150 STSs
from community and local efforts (abs. 55); this would provide
at least 40% of the number required for the complete map of
the X chromosome. In other efforts that assemble contigs on
the basis of fingerprinting with inter-Alu or repetitive sequence
probes, the contig coverage can be complemented with STSs
derived from YACs or from independent sources. Along with
the use of some YACs and probes in common, this provides a
straightforward route to the integration of cloned coverage
from various sources.
YACs are now providing long-range coverage of nearly all
of the chromosome. In the longest stretch of DNA that is
poorly cloned into YACs (about 1.5 Mb in subtelomeric Xq28),
cosmids have been assembled (abs. 86) that provide the current
map; and bacterial clones of various types (P1, BAC, PAC,
etc.) can very likely provide comparable supplements to other
more delimited zones of poor YAC coverage. Once again, the
provision of resources -is critical, particularly of high quality
clones like the X-specific cosmid collection from the Lawrence
Livermore Laboratory.
The next stage of efforts will involve the continuation of
map closure while mapping merges increasingly with
sequencing and gene-finding efforts. As in the case of long-
range mapping, a number of approaches are currently being
tested to verify maps and to reach analyses at higher resolution.
They include comparative analysis of marker content in
somatic cell hybrids and radiation hybrids (for example, Gorski
et al., 1992; Peterlin et al., 1993), which can be combined with
rare-cutter restriction mapping (O'Reilly et al., 1993); and theuse of favorable patient material (Goyns et al., 1993; abs. 6). A
fruitful approach to the higher resolution analysis of YAC-
based contigs is to recover cosmids or other bacterial clones
that provide another layer of the map, either by screening
cosmid libraries or by subcloning YACs (abs. 5, 6 and 86;
Holland et al., 1993; Buxton et al., 1993; Whitaker et al., 1993;
Zuo et al., 1993).
Map assembly and closure can also be aided by
comparative mapping. Progress on mapping of the mouse X
chromosome was detailed by Brown and colleagues (abs. 10),
by Boyd et al. (abs. 9), and by Pragliola et al. (abs. 60),
including specific examples where information on clones in
mouse was helpful to assembly of the human map. The current
mouse X chromosome map has been summarized by Herman et
al. (1994). Evolutionary comparisons in eutherian mammals
and in marsupials are also useful to understand specific
biological phenomena, such as X inactivation and sex
determination (abs. 4, 17, 18 and 33).
YACs or cosmids provide substrates both for gene finding
by a variety of means, including direct sequencing, with a
useful modification of previous methods proposed by Fontes
and colleagues (abs. 27). Such biological work clearly
occupies a growing fraction of the attention of the community,
both in respect to disease genes and in respect to genes in
general. The placement of ESTs on the map (Parrish and
Nelson, 1993) is now being abetted by searches for motifs and
BLOCKS as mapping tools (D'Esposito et al., 1994), including
the examination, for example, of cDNAs containing triplet-
repeat elements (Li et al., 1993). The body of this report
summarizes further some of the ongoing efforts to locate more
genes, along with the first push toward long-range sequencing.
About 600 kb of sequence has been accumulated in the last
year, primarily from intervals in Xq27.3-q28 (see figure 2), and
more extensive efforts are now beginning.
Genetic maps and new microsatellite
polymorphisms
Several overall genetic maps of the X chromosome have
been constructed. The initial Genethon map included 25 X-
linked Afm microsatellite markers that are now well integrated
with other markers in regional physical or genetic maps. The
second generation Genethon map contains 80 Afm markers
extending over 166 cM (Gyapay et al., 1994). Many of the
new markers have also been integrated in YAC contigs or in
various regional maps (see below and figure 1). These markers
have also been used to screen the CEPH megaYAC library
(Cohen et al., 1993). However, the Genethon map contains
many clusters of unresolved markers, due to the relatively
small number of CEPH families genotyped in that effort. The
largest gaps have a length of 13 cM (in Xq24-q25) and 17 cM
(in Xq27) (Gyapay et al., 1994). The latter may correspond to a
region of higher recombination. The 236 cM map of Donnelly
et al. (1994), initially reported at XCW4, contains 62 PCR-
based marker loci, 30 of which were uniquely ordered in a
framework map. Using data in the CEPH data base and
genotypes generated on 15 CEPH families by the Cooperative1
'-I
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Willard, H. F.; Cremers, F.; Mandel, J. L.; Monaco, A. P.; Nelson, D. L. & Schlessinger, D. Report of the fifth international workshop on human X chromosome mapping, report, December 31, 1994; St. Louis, Missouri. (https://digital.library.unt.edu/ark:/67531/metadc681340/m1/2/: accessed April 24, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT Libraries Government Documents Department.