Talk:Human genome

quality

according to the url below, a paper from top experts in a top journal (ie highly authoritative) says that there are many many gaps (unsequenced) regions in the human genome imo, the lack of attention paid to these gaps is somewhat misleading for the general public; eg when scientists use the word "complete" it means, per the dictionary, that we have no gap, no missign sequence genome yet this is empirically false http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13907.html

Number of genes

We don't know the exact number of genes in the human genome. There are at least 19,000 protein-coding genes and no more than 20,000. The number of noncoding genes is all over the map. There are only a few thousand (at most!) that have been confirmed as real genes but there are many more transcribed regions that some scientists call genes even though they have not been shown to have a function. This is a problem since the definition of a gene requires that it produce a FUNCTIONAL product.

The number of noncoding genes predicted by Ensembl is down to 25,967 in the latest annotation (CRCh38.13) but most of those are stretches of DNA that produce lncRNAs that have not been shown to have a function.

The issue was raised last year (see Noncoding DNA above) but not resolved. We need to present a consistent view of the number of genes in this article and we need to point out the controversy over the number of noncoding genes. Genome42 (talk) 14:41, 26 June 2023 (UTC)

Chromosome table

The data in the large table on individual chromosomes is ten years old. Not only does it contain outdated information and unfounded speculation but it's also far too complicated and specific for a Wikipedia article.

I think we should remove it. What do others think? Genome42 (talk) 14:49, 26 June 2023 (UTC)

Reorganization

I suggest that we reorganize the entire article to eliminate redundancy and conflicting information. I think we should begin by moving some information out of the introduction and putting it into the main body of the article.

I think the main subsections should be:

          Size of the human genome
          Content of the human genome
          Sequencing the human genome
          Information content (in bits)
          Genomic variation in humans
          Personal genomics
          Human genetic disorders (including gene knockouts)
          Evolution
          Mitochondrial DNA
          Epigenome
Genome42 (talk) 18:12, 6 July 2023 (UTC)

The section on content could have the following subsections:

          Protein-coding genes

          Non-coding genes

          Regulatory sequences

          Centromeres and telomeres

          Other functional elements

          Pseudogenes

          Transposons and viruses

          Junk DNA

If there are no objections, I'll begin by moving the current content into the new subsections. Then we can edit the information to make it more consistent and more readable. Genome42 (talk) 18:17, 6 July 2023 (UTC)

3,054,815,472

3,054,815,472 base pairs? The box claims 3,117,275,501. Neither are, of course, right (or maybe both are). Why not give a little credit to the readers and presume that they can handle a bit of complexity? Like saying the number of base pairs is determined using a specific individual's dna (or a group of specific individuals). Why not mention that while we're a diploid species, as far as known we all contain tetraploid and octaploid cells? (This is true, I'm guessing, after a number of cell divisions in the embryo.) Why not say the reference dna is normally selected to be typical and avoids individuals with known aneuploidy, euploidy (except as mentioned), and sex chromosome (rare) variations. In counting the base pairs, there are errors, and any two (independent) researchers are NOT likely to come up with the same exact number, even if the same reference dna is used? Why not say that doing a complete genome is very, very difficult? (I'm not sure that it's ever been fully done ("fully" means counting all base pairs in one lab, by one group of researchers). Also, why not mention that even a reference person will have a number of mutations in their cells (those with nuclei) so that even "their" genome doesn't fully describe their "complete set"?98.21.208.178 (talk) 07:13, 28 February 2024 (UTC)

I tried to fix this and started the reorganization that I suggested in July 2023. Genome42 (talk) 23:09, 28 February 2024 (UTC)

Definition of "genome"

The very first sentence of the article defines the human genome as, "The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei ..." Except for the ambiguous use of 'pairs,' this is a correct definition that corresponds to the definition in genome, "... the 'genome' refers to only one copy of each chromosome."

A recent edit introduced the term "haploid genome." This is equivalent to saying "haploid set of one copy of each chromosome" and that makes no sense. The phrase "diploid genome" is even worse since it implies that there are different kinds of genomes; haploid, diploid, and polyploid. There can be haploid, diploid, and polyploid sets of chromosomes but not genomes.

I made the appropriate edits. Genome42 (talk) 16:06, 19 September 2024 (UTC)