Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

A <i>COLQ</i> Missense Mutation in Labrador Retrievers Having Congenital Myasthenic Syndrome

<div><p>Congenital myasthenic syndromes (CMSs) are heterogeneous neuromuscular disorders characterized by skeletal muscle weakness caused by disruption of signal transmission across the neuromuscular junction (NMJ). CMSs are rarely encountered in veterinary medicine, and causative mutations have only been identified in Old Danish Pointing Dogs and Brahman cattle to date. Herein, we characterize a novel CMS in 2 Labrador Retriever littermates with an early onset of marked generalized muscle weakness. Because the sire and dam share 2 recent common ancestors, CMS is likely the result of recessive alleles inherited identical by descent (IBD). Genome-wide SNP profiles generated from the Illumina HD array for 9 nuclear family members were used to determine genomic inheritance patterns in chromosomal regions encompassing 18 functional candidate genes. SNP haplotypes spanning 3 genes were consistent with autosomal recessive transmission, and microsatellite data showed that only the segment encompassing <i>COLQ</i> was inherited IBD. <i>COLQ</i> encodes the collagenous tail of acetylcholinesterase, the enzyme responsible for termination of signal transduction in the NMJ. Sequences from <i>COLQ</i> revealed a variant in exon 14 (c.1010T>C) that results in the substitution of a conserved amino acid (I337T) within the C-terminal domain. Both affected puppies were homozygous for this variant, and 16 relatives were heterozygous, while 288 unrelated Labrador Retrievers and 112 dogs of other breeds were wild-type. A recent study in which 2 human CMS patients were found to be homozygous for an identical <i>COLQ</i> mutation (c.1010T>C; I337T) provides further evidence that this mutation is pathogenic. This report describes the first <i>COLQ</i> mutation in canine CMS and demonstrates the utility of SNP profiles from nuclear family members for the identification of private mutations.</p></div

Multigenerational pedigree of Labrador Retrievers.

<p>Filled individual icons denote affected dogs and semi-filled icons denote obligate carriers. Asterisks mark individuals selected for whole-genome SNP profiling.</p

Microsatellite and SNP haplotypes (color-coded bars below individuals) are shown for 3 candidate genes.

<p>Positions (in Mb) are according to CanFam 2. Filled individual icons denote affected dogs and semi-filled icons denote obligate carriers. Chromosome 23 haplotypes (blue) are inherited IBD in both affected dogs.</p

(A) Sequence from the 5′ end of the C-terminal domain of ColQ in mammals.

<p>Identical residues are denoted by an asterisk, conserved substitutions by a colon, and semi-conserved substitutions by a period. Residues altered in human CMS cases are highlighted in yellow <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106425#pone.0106425-Mihaylova1" target="_blank">[4]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106425#pone.0106425-Ohno2" target="_blank">[30]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106425#pone.0106425-Nakata1" target="_blank">[32]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106425#pone.0106425-Wargon1" target="_blank">[37]</a>. (B) BtsI digest results for the Labrador Retriever family. PCR amplicons from <i>COLQ</i> exon 14 are 470 bp in size and cleaved into 204 and 266 bp fragments in the presence of c.1010T>C. Three clinically normal littermates were identified as carriers, denoted by semi-filled icons.</p

Repetitive stimulation of the peroneal motor nerve of an affected Labrador Retriever at 2 Hz (A), 5 Hz (B), and 50 Hz (C).

<p>Decrement of the CMAP was observed at all tested frequencies. Sweep speed and sensitivity settings are identical to those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106425#pone-0106425-g002" target="_blank">Figure 2</a>. Control tracings are from the peroneal nerve of a healthy 5 month old Beagle with no decrement seen at low frequency stimulation and normal pseudofaciliation (CMAP gets taller and narrower) with tetanic stimulation.</p