The DNA sequence of the human X chromosome

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

A physical map of the human genome

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence

BACKGROUND

The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were widely debated in the genomics community: how correct is the sequence with respect to base-pair (bp) accuracy and frequency of assembly errors? And, how difficult is it to bring a WGS sequence to the accepted standard for finished sequence? We are now in a position to answer these questions.

RESULTS

Our finishing process was designed to close gaps, improve sequence quality and validate the assembly. Sequence traces derived from the WGS and draft sequencing of individual bacterial artificial chromosomes (BACs) were assembled into BAC-sized segments. These segments were brought to high quality, and then joined to constitute the sequence of each chromosome arm. Overall assembly was verified by comparison to a physical map of fingerprinted BAC clones. In the current version of the 116.9 Mb euchromatic genome, called Release 3, the six euchromatic chromosome arms are represented by 13 scaffolds with a total of 37 sequence gaps. We compared Release 3 to Release 2; in autosomal regions of unique sequence, the error rate of Release 2 was one in 20,000 bp.

CONCLUSIONS

The WGS strategy can efficiently produce a high-quality sequence of a metazoan genome while generating the reagents required for sequence finishing. However, the initial method of repeat assembly was flawed. The sequence we report here, Release 3, is a reliable resource for molecular genetic experimentation and computational analysis.

A BAC-based physical map of the major autosomes of Drosophila melanogaster

We constructed a bacterial artificial chromosome (BAC)-based physical map of chromosomes 2 and 3 of Drosophila melanogaster, which constitute 81% of the genome. Sequence tagged site (STS) content, restriction fingerprinting, and polytene chromosome in situ hybridization approaches were integrated to produce a map spanning the euchromatin. Three of five remaining gaps are in repeat-rich regions near the centromeres. A tiling path of clones spanning this map and STS maps of chromosomes X and 4 was sequenced to low coverage; the maps and tiling path sequence were used to support and verify the whole-genome sequence assembly, and tiling path BACs were used as templates in sequence finishing.

The DNA sequence, annotation and analysis of human chromosome 3

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

The finished DNA sequence of human chromosome 12

Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.

Dosimetry and physical treatment planning for iodine eye plaque therapy

The dosimetry of eye plaques loaded with iodine-125 seeds (type 6702) was performed by means of computer calculations and measurements with thermoluminescent dosimeters (TLD). Measurements of the depth dose distribution (2-25.5 mm) along the transverse axis of a single seed were performed in water equivalent phantom material. The transverse axis attenuation and geometry factor F(r) was obtained by applying a least squares fit to the measured data. Based on the resulting radial dose function, a computer program was developed which calculates dose distributions within the eye for arbitrary loading and placement of the eye plaque. The computational results were verified by TLD measurements in an eye phantom.

Autoradiography for iodine-125 seeds

To study the interior design of model 6702 and 6711 iodine-125 seeds contact autoradiographs were performed using mammography film. Improved resolution was obtained using a pin-hole camera with a hole of 0.1 mm x 0.1 mm. With these techniques, qualitative determination of the relative activity distribution within each seed was possible. The number of the activated resin spheres and the positions of the centers of these spheres can be exactly determined. A model calculation shows, that variations in the arrangement of the activated spheres within a seed have a moderate influence on the dose distribution at source distances below 10 mm. Knowing the exact source configuration may be useful when comparing dose calculations with measured data for model 6702 125I seeds which are currently employed in ophthalmic plaque and implant therapy of other tumors.

Solid phantom material for the dosimetry of iodine-125 seed ophthalmic plaques

PURPOSE

A tissue-equivalent solid phantom material, RE-1, closely simulating the radiological attenuation and scattering properties of the human eye for the iodine-125 photon spectrum and their Compton-scattered secondary photons, was fabricated on a polyethylene base with CaCO3 and MgO as inorganic additives.

METHODS AND MATERIALS

A 24 mm diameter spherical phantom was made from 1.1 mm thick sheets of RE-1, and holes were drilled in which 1 mm3 TLD cubes were placed.

RESULTS

The radial dose function g(r), which determines the dose profile on the transverse axis, was measured in a quasi-infinite phantom of RE-1.

CONCLUSION

The values obtained deviate only slightly from those for a quasi-infinite phantom made from water-equivalent material.

[Aspects of the computer-assisted irradiation planning for the HDR (high dose rate) afterloading technique]

A mathematical optimization method will be discussed concerning the three dimensional radiation treatment planning of the HDR-afterloading technique. Program libraries of the EDV Center of the University of Essen were used.