On June 26, , the International Human Genome Sequencing Consortium announced the production of a rough draft of the human genome sequence. In April, , the International Human Genome Sequencing Consortium is announcing an essentially finished version of the human genome sequence. This version, which is available to the public, provides nearly all the information needed to do research using the whole genome. The difference between the draft and finished versions is defined by coverage, the number of gaps and the error rate.
The draft sequence covered 90 percent of the genome at an error rate of one in 1, base pairs, but there were more than , gaps and only 28 percent of the genome had reached the finished standard.
In the April version, there are less than gaps and 99 percent of the genome is finished with an accuracy rate of less than one error every 10, base pairs. The differences between the two versions are significant for scientists using the sequence to conduct research.
Every part of the genome sequenced by the Human Genome Project was made public immediately, and new information about the genome is posted almost every day in freely accessible databases or published in scientific journals which may or may not be freely available to the public.
The Supreme Court ruled in that naturally occurring human genes are not an invention and therefore cannot be patented.
However, private companies can apply for patents on edited or synthetic genes, which have been altered significantly from their natural versions to count as a new, patentable, product. The Human Genome Project could not have been completed s quickly and as effectively without the strong participation of international institutions.
However, almost all of the actual sequencing of the genome was conducted at numerous universities and research centers throughout the United States, the United Kingdom, France, Germany, Japan and China.
In , Congress established funding for the Human Genome Project and set a target completion date of Additionally, the project was completed more than two years ahead of schedule. It is also important to consider that the Human Genome Project will likely pay for itself many times over on an economic basis - if one considers that genome-based research will play an important role in seeding biotechnology and drug development industries, not to mention improvements in human health.
Since the beginning of the Human Genome Project, it has been clear that expanding our knowledge of the genome would have a profound impact on individuals and society. The leaders of the Human Genome Project recognized that it would be important to address a wide range of ethical and social issues related to the acquisition and use of genomic information, in order to balance the potential risks and benefits of incorporating this new knowledge into research and clinical care.
The United States Congress mandates that no less than five percent of the annual NHGRI budget is dedicated to studying the ethical, legal and social implications of human genome research, as well as recommending policy solutions and stimulating public discussion.
The ELSI program at NHGRI, which is unprecedented in biomedical science in terms of scope and level of priority, provides an effective basis from which to assess the implications of genome research. Among these are major changes to the way investigators and institutional review boards handle the consent process for genomics studies.
The ELSI program has been effective in promoting dialogue about the implications of genomics, and shaping the culture around the approach to genomics in research, medical, and community settings.
Because the human genome sequence is intended to serve as a permanent foundation for biomedical research, it was important to assess its quality and to characterize its remaining defects. For this purpose, we used a number of comparisons and consistency checks. Tests of accuracy were designed to detect potential problems that may have occurred in clone-based sequencing. This may include errors in assembling the finished sequence within individual clones, and errors in concatenating adjacent finished clones to create the final product.
The analysis was complicated by the presence of polymorphism in the human population, because differences between sequence clones may reflect either errors or polymorphism. Independent quality assessment. In the final stages, an independent group examined a random sample of finished clones by generating additional data and generating new assemblies Mb and found an error rate of 1.
The small events consisted largely of single-base substitutions, whereas the remaining small and large events primarily concerned the number of consecutive copies of a tandem repeat Analysis of clone overlap. Mb , by examining overlapping sequence between consecutive finished large-insert clones.
If two such clones derive from the same copy of the human genome, any sequence differences in the overlap must reflect an error in one of the two clones. By comparing independent clones, this quality assessment method also has the ability to detect cloning artefacts. We examined 4, substantially overlapping clones derived from the same library; half are expected to be derived from the same haplotype and half from a different haplotype. The resulting distribution Fig.
The number of single-base differences in overlaps for clones from the same library and from different libraries is plotted. The results are consistent with half of the clones from the same library representing identical underlying DNA sequence with low error rate, and half representing different haplotypes as expected.
The number of indels per? We then examined overlapping clones likely to be from the same haplotype with no single-base mismatches and counted the discrepancy rate for indels Fig. By contrast, clones from different libraries show a discrepancy rate that is at least fold higher. Overall, the analysis indicates that the overall error rate reflecting both sequence error and cloning artefacts is 20—fold lower than the human polymorphism rate.
Analysis of junctions. We assessed longer-range integrity of the genome sequence by studying read pairs from large insert clones. Fosmid clones are particularly useful because their insert sizes cluster tightly around 40? We aligned the fosmid end sequences to the genome sequence. Some fosmids could not be uniquely placed because one or both ends consisted almost entirely of repeat sequence.
Using the uniquely placed fosmids which provide about eightfold clone coverage of the euchromatic genome , we sought to obtain independent confirmation of the order, orientation and adjacency of the junction between consecutive finished large-insert clones used to construct the genome sequence. About half of the remaining junctions were supported by fosmids with unique placement at one end but multiple placements at the other end.
Overall, the analysis provided strong support for accuracy of the junctions underlying the current genome sequence. Search for deletions. We next scanned the genome sequence for evidence of deletions of several kilobases in size, using the same fosmid data set. Such differences could reflect either an error in the genome sequence, a deletion in the fosmid clone, or a deletion polymorphism between the DNA sources. Because the methodology cannot detect deletions larger than a fosmid, we also analysed discrepant fosmid links, which could reflect deletions.
See Methods in Supplementary Information. The top portion shows fosmids along a region of chromosome 10 centred at nucleotide 46,, , mapped by virtue of their paired-end sequences. The difference between inferred length, calculated from the location of fosmid ends in finished sequence, and average length for the entire library, is shown to the right of each clone.
For each point, the standard deviation of the local average difference for all spanning fosmids is plotted below; the threshold of 3. The region from 45 to 55? Comparison with available chimpanzee sequence further localized the difference vertical line. The majority of length differences detected by this analysis appear to represent polymorphisms, not sequence errors. These regions were then scrutinized by alignment with the recently obtained draft sequence of the chimpanzee genome R. Waterston, personal communication.
Roughly two-thirds appear to represent polymorphic deletions in the human population and one-third represent actual errors in the current genome sequence. Analysis of a larger collection of fosmids could probably pinpoint the majority of these errors, allowing them to be corrected. Tests of coverage were designed to measure the proportion of the euchromatic genome missing from the current genome sequence, by assessing the presence of independently sampled human sequences such as complementary DNA clones and random genomic clones.
Analysis of cDNAs. The analysis 35 involved 17, distinct gene loci spanning ? Mb of genomic sequence. The vast majority A few of these 0. A few others 0. We examined the remaining cases 0. The cDNA sequence appeared to be completely absent in 0. For almost all of completely absent cDNAs, the genomic location of the gene was known or could be inferred and corresponds to a gap in the current genome sequence. For the partially absent cDNAs, more than half of the cases lie adjacent to gaps.
The remainder may represent either errors in the current genome sequence or polymorphic deletions; these are being investigated further. Overall, the proportion of cDNA sequence that is missing from the genome sequence is only 0. This may underestimate the proportion of genome missing from the finished sequence, however, because focused efforts were made to capture genomic sequence containing missing messenger RNAs.
Analysis of random genomic plasmids. As an additional and broader test of coverage, we analysed paired end-sequences from 5, small-insert 3—4? After excluding heterochromatic repeats and other artefacts, we found that For 0. For another 0. The current genome sequence contains gaps, which could not be closed with available techniques. We briefly describe the nature of these gaps and discuss the prospects for eventual closure.
See Supplementary Information Notes 2 and 4. Heterochromatic regions 33 gaps. The heterochromatic regions of the human genome were not targeted by the HGP, because their highly repetitive properties make them largely refractory to current cloning and sequencing strategies.
There are 33 heterochromatic regions falling into four types. The three secondary constrictions are immediately adjacent to the centromere on chromosome arms 1q, 9q and 16q and contain various satellite repeats beta, gamma, satellite I, II, III. Finally, there is a single large region on distal Yq composed primarily of thousands of copies of several repeat families. The heterochromatic regions all tend to be highly polymorphic in length in the human population.
Euchromatic boundary regions 35 gaps. The euchromatic regions of the human genome are bounded proximally by heterochromatin and distally by a telomere consisting of several kilobases of the hexamer repeat TTAGGG.
We examined the current genome sequence for evidence of the expected boundaries on the 43 euchromatic arms. See Supplementary Information Note 4. At the proximal ends, 30 of the 43 cases show sequence characteristic of either heterochromatin or immediately flanking regions such as higher-order centromeric repeats, stretches of at least 10? We cannot exclude the possibility that there is additional unique sequence between this point and the proximal heterochromatin; but efforts to extend the finished sequence further were unsuccessful.
In the remaining 13 cases, the finished sequence contains no evidence of heterochromatin-related sequence. At the telomeric ends, 21 of the 43 cases show continuous sequence extending to the telomeric repeat.
This sequence was typically obtained by isolation and sequencing of half-YAC clones spanning to the telomere An additional 18 cases are sequence gaps, in which half-YACs reaching to the telomere were isolated but finished sequence could not be obtained.
The remaining four cases are physical gaps, in which large-insert clones extending to the telomere could not be obtained. Euchromatic interior regions gaps. The remaining gaps are located within the current genome sequence. These consist of physical gaps for which no clones could be isolated, and 58 sequence gaps for which clones were found but reliable finished sequence could not be obtained.
The physical gaps are greatly enriched in regions of segmental duplication Fig. Such segmental duplications are especially frequent in pericentromeric regions, and gaps are notably more frequent in these regions. The association of gaps with segmental duplications is examined in detail elsewhere Large duplications are shown to approximate scale; smaller ones are indicated as ticks. Sequence gaps are indicated above the chromosomes in red. Unfinished clones are indicated as black ticks. The blue bars show the result of direct analysis of near-complete sequence.
The gold bars show an independent estimate 65 using whole-genome shotgun data to correct for potential mis-assembly of such segmental duplications. The strong agreement suggests that most segmental duplications are properly represented in near-complete genome sequence. The discrepancy for chromosome X is probably a result of errors in the independent estimate, due to limited coverage and diversity of data from this chromosome The most extreme case occurs near the centromere of chromosome 9.
The most proximal 5? Mb on 9p and 4? Mb on 9q comprise a mere 0. These two pericentric regions are unique in the genome with respect to density of segmental duplication and the average degree of intrachromosomal sequence identity Other proximal regions also show a higher-than-average density of gaps.
For example, the proximal 2? Mb on the remaining 41 euchromatic arms comprise 2. Nearly all of these proximal gaps are flanked by segmental duplications Fig. There is also a clustering of such gaps in subtelomeric regions.
The terminal 1? Mb on the 43 euchromatic arms represents 1. The most proximal regions are crowded with alpha satellite sequences and other centromeric repeats; composition, density and order may vary considerably between chromosome arms Just outside this region, there is usually a high density of inter- and intra-chromosomal duplication. For details, see text and refs 39, 40, 66 and The terminal repeat tract consists of 2—15?
Short 50—? Proximal to the Srpt region is chromosome-specific genomic DNA, typically with a high GC content and high gene density. Stretches of segmentally duplicated DNA that occur only once within subtelomeric regions tan are interspersed with 1-copy subtelomeric DNA yellow in a telomere-specific fashion.
Closing the remaining gaps. These represent regions that could not be reliably mapped, cloned and sequenced with current methods. Rather than applying further brute force, it is now time to develop focused strategies to resolve the regions. The remaining euchromatic gaps probably reflect two major issues. The first pertains to regions harbouring segmentally duplicated sequence.
Such regions are challenging to map because it can be extremely difficult to discern whether two clones with small sequence differences represent different loci or different alleles at a single locus. This challenge was eventually resolved for chromosome Y ref.
By using DNA from a single haploid source, it was possible to rely on differences at only a handful of nucleotides to distinguish repeated sequences. This approach could be applied to the rest of the genome by using appropriate haploid sources, such as a hydatidiform mole or monochromosomal hybrids. In both instances, use of parental controls to guard against being misled by somatic rearrangements would be well advised. It may be useful to test these approaches on individual chromosomes.
The second issue is that some gaps are likely to correspond to regions that cannot be efficiently propagated in current large-insert vectors and hosts. It may be useful to test new kinds of large-insert libraries for clones containing unique sequences not contained in the current human genome sequence perhaps seeded by probes derived from random small-insert genomic plasmids, as discussed above. In addition, genome completion may benefit from long-range mapping techniques such as optical mapping 38 , which may provide independent information about difficult regions.
Completing the euchromatic sequence is an important goal, but is clearly now a research effort rather than a high-throughput project. Sequencing the human heterochromatin poses an even greater challenge. The current human sequence penetrates only the periphery of the heterochromatin—for example, the pericentric regions on a few chromosome arms 39 , This progress has required concerted efforts with specialized mapping techniques and painstaking assembly.
The fundamental issue is that current shotgun strategies are poorly suited to assembling large, highly repetitive regions. The hierarchical shotgun strategy faces the challenge of accurate assembly of individual BACs and accurate overlap of BAC clones, with the underlying data consisting of nearly identical sequence; the whole-genome shotgun strategy compounds these problems.
Conceivably, the hierarchical strategy could be adapted as was done for repetitive regions of chromosome Y. Approaches might include the use of the following: haploid DNA sources to restrict the problem to a single haplotype; single chromosome sources to avoid confusion among related centromeres on different chromosomes; sheared BAC libraries to avoid biases caused by the unusual distribution of restriction sites within the repeat sequences; assembly based on rare base differences that distinguish near-identical repeats; cloning vectors that minimize rearrangements; and subclone libraries of varying insert lengths.
Such an approach will also require ensuring accurate recovery and stability of heterochromatic regions in large-insert clones. Even so, the path is likely to be arduous and expensive to obtain regions of uncertain information content.
Alternatively, it may be possible to develop new approaches. These might include methods to obtain much longer effective read lengths, directed reads from known locations and long-range mapping information about the location of rare base differences among repeat copies such as optical mapping 38 or padlock probes The present genome sequence enables far more precise analyses of the human genome, especially those that depend sensitively on high accuracy and near-completeness.
Rather than revisit all of the analyses in our initial analysis of the human genome, we have chosen four examples that illustrate the utility of the current near-complete sequence.
The human genome is notable for its high proportion of recent segmental duplications. They are of great medical interest because their unusual structure often predisposes them to deletion or rearrangement with consequent phenotypic effects; prominent examples include the Williams syndrome region 7q , Charcot—Marie—Tooth region 17p , DiGeorge syndrome region 22q and the AZF-C region Y Some regions of segmental duplication have also recently been shown to be evolutionary nurseries in which coding sequences are undergoing strong positive selection Accurate analysis of segmental duplications was previously impossible because the draft sequence also contained a high degree of artefactual duplication.
This difficulty was recognized at the time and the approximate proportion of true and artefactual duplication was inferred indirectly. Co-expression of fibulin-5 and VEGF increases long-term patency of synthetic vascular grafts seeded with autologous endothelial cells. Gene Ther. Plasma and urinary metabolomic profiles of Down Syndrome correlate with alteration of mitochondrial metabolism. Integrated quantitative transcriptome maps of human trisomy 21 tissues and cells.
Front Genet. Systematic reanalysis of partial trisomy 21 cases with or without Down Syndrome suggests a small region on 21q Hum Mol Genet. Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome. Physiol Genomics. BMC Bioinformatics. GeneBase 1. Database Oxford. Bogenhagen DF. Mitochondrial DNA nucleoid structure. Biochim Biophys Acta. Structural and compositional features of untranslated regions of eukaryotic mRNAs.
Int J Mol Med. Molecular structure of a double helical DNA fragment intercalator complex between deoxy CpG and a terpyridine platinum compound. Download references. AP developed the software, collected the data, performed the analysis, and wrote the manuscript draft. MCP and FA collected the data and critically revised the results of the analysis. PS designed the work, tested the software and wrote the manuscript draft. MC and LV supervised the project and critically revised the manuscript.
All authors contributed to the interpretation of data. All authors read and approved the final manuscript. We wish to sincerely thank the Fondazione Umano Progresso, Milano, Italy for their fundamental support to our research on trisomy 21 and to this study.
We thank all the other people that very kindly contributed by individual donations to support part of the fellowships as well as hardware and software. Some of them are also are available within the article and its additional information files. Minimum software requirements: Mac OS X Minimum system requirements: Mac OS X A connection to the Internet is required to display the software tutorial and to download data for set up, but not to run the tool.
This work was supported by donations from Fondazione Umano Progresso and from other donors acknowledged below which supported the purchase of the hardware and software that were necessary to conduct the research.
The funding sources had no role in the design of this study and collection, analysis, and interpretation of data and in writing the manuscript. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. You can also search for this author in PubMed Google Scholar. Correspondence to Maria Caracausi.
Human genome length and weight calculations, human GC content analysis and GC content analysis in other species. Detailed description of the genome length and weight calculations and of the GC content analysis for the human genome and for Danio rerio , Caenorhabditis elegans , Saccharomyces cerevisiae , and Escherichia coli.
Nucleotide counts in the 24 human chromosomes and estimation of uncertain bases, based on GRCh Nucleotide counts for the 24 human chromosomes and estimation of uncertain bases necessary for the genome length and weight calculations and for the GC content analysis, based on the most recent human genome assembly, obtained as described in detail in Additional file 1 : Additional Methods file.
Nucleotide counts for the 24 human chromosomes and estimation of uncertain bases necessary for the genome length and weight calculations and for the GC content analysis, based on the previous human genome assembly, obtained as described in detail in Additional file 1 : Additional Methods file.
Length, weight and GC content of human chromosomes, genome and mitochondrial DNA, based on the previous human genome assembly, obtained as described in detail in Additional file 1 : Additional Methods file.
Accordance of our calculations with previous reports. Accordance with previous reports of our calculations of the number of chromosomes and the total genome length for Danio rerio , Caenorhabditis elegans , Saccharomyces cerevisiae , and Escherichia coli obtained as described in detail in Additional file 1 : Additional Methods file.
Reprints and Permissions. Piovesan, A. On the length, weight and GC content of the human genome. BMC Res Notes 12, Download citation. Received : 07 December Accepted : 15 February Published : 27 February Anyone you share the following link with will be able to read this content:.
Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative. Skip to main content. Search all BMC articles Search. The DNA that makes up all genomes is composed of four related chemicals called nucleic acids — adenine A , guanine G , cytosine C , and thymine T. At the time, researchers thought they knew enough about how DNA worked to search for the functional units of the genome, otherwise known as genes.
A gene is a string of DNA that encodes the information necessary to make a protein, which then goes on to perform some function within our cells. After the Human Genome Project, scientists found that there were around 20, genes within the genome, a number that some researchers had already predicted.
Imagine being given multiple volumes of encyclopedias that contained a coherent sentence in English every pages, where the rest of the space contained a smattering of uninterpretable random letters and characters. You would probably start to wonder why all those random letters and characters were there in the first place, which is the exact problem that has plagued scientists for decades.
Why is so much of our genome not being used to code for protein? Does this extra DNA serve any functional purpose? To start to get an idea of whether we need all of this extra DNA, we can look at closely related species that have wildly varying genome sizes.
For instance, the genus Allium , which includes onions, shallots, and garlic, has genome sizes ranging anywhere from 10 to 20 billion base pairs. It is very unlikely that such a large amount of extra DNA would be useful in one species and not in its genetic cousin, perhaps arguing that much of the genome is not useful []. Furthermore, these genomes are much larger than the human genome, which indicates either that an onion is highly complex, or more likely that the size of a genome says nothing about how complex the organism is or how it functions.
Due to amazing technological advances in sequencing DNA and in using computers to help analyze the resulting sequences collectively known as bioinformatics , large-scale projects similar to the Human Genome Project have begun to unravel the complexity and size of the human genome. In other words, while the Human Genome Project set out to read the blueprints of human life, the goal of ENCODE was to find out which parts of those blue prints actually do something functional.
Just this month, the consortium published its main results in over 30 scientific journal articles, and it has been given a significant amount of attention by the media []. Figure 1.
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