Chromosome abnormality

chromosomal abnormalitieschromosome abnormalitieschromosomal abnormality
A chromosomal disorder, anomaly, aberration, or mutation is a missing, extra, or irregular portion of chromosomal DNA. It can be from a typical number of chromosomes or a structural abnormality in one or more chromosomes. Chromosome mutation was formerly used in a strict sense to mean a change in a chromosomal segment, involving more than one gene. The term "karyotype" refers to the full set of chromosomes from an individual; this can be compared to a "normal" karyotype for the species via genetic testing. A chromosome anomaly may be detected or confirmed in this manner. Chromosome anomalies usually occur when there is an error in cell division following meiosis or mitosis.

Topologically associating domain

Topologically Associating Domainslamina-associated domainsTAD
A topologically associating domain (TAD) is a self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD. These three-dimensional chromosome structures are present in animals as well as some plants, fungi, and bacteria. In bacteria, they are referred to as Chromosomal Interacting Domains (CIDs). TADs can range in size from thousands to millions of DNA bases. The functions of TADs are not fully understood, but in some cases, disrupting TADs leads to disease because changing the 3D organization of the chromosome disrupts gene regulation.

Oryzomys couesi

Coues' rice ratO. couesiCoues's rice rat
The karyotype includes 56 chromosomes and a fundamental number of 56 autosomal arms (2n = 56, FNa = 56). The autosomes include 26 pairs of acrocentric chromosomes, with a long and a very short arm, and one medium-sized submetacentric pair, with one arm shorter than the other. The X chromosome is either acrocentric, with a long and a short arm, or subtelocentric, with a long and a vestigial arm. The form of the sex chromosomes has been used to distinguish the marsh rice rat from Oryzomys couesi, but there are no consistent differences between the two.

Genetic marker

genetic markersmarkermarkers
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites. For many years, gene mapping was limited to identifying organisms by traditional phenotype markers. This included genes that encoded easily observable characteristics such as blood types or seed shapes.

Fluorescence in situ hybridization

FISHfluorescent in situ hybridizationfluorescence ''in situ'' hybridization
Fluorescence in situ hybridization (FISH) is a molecular cytogenetic technique that uses fluorescent probes that bind to only those parts of a nucleic acid sequence with a high degree of sequence complementarity. It was developed by biomedical researchers in the early 1980s to detect and localize the presence or absence of specific DNA sequences on chromosomes. Fluorescence microscopy can be used to find out where the fluorescent probe is bound to the chromosomes. FISH is often used for finding specific features in DNA for use in genetic counseling, medicine, and species identification.

Plant genome assembly

Due to their complexity, the plants’ genome sequences can't be assembled back into chromosomes using only short reads provided by next-generation- sequencing technologies (NGS), and therefore most plant genome assemblies available that used NGS alone are highly fragmented, contain large numbers of contigs, and genome regions are not finished. Highly repetitive sequences, often larger than 10kbp, are the main challenge in plants. Most of the chromosomal sequences are produced by the activity of mobile genetic elements (MGEs) in the plant genomes. MGEs are divided into two classes: class I or retrotransposons, and class II or DNA transposons.

Gene map

mapmapping
FISH is a method used to detect the presence (or absence) of a DNA sequence within a cell. DNA probes that are specific for chromosomal regions or genes of interest are labeled with fluorochromes. By attaching fluorochromes to probes, researchers are able to visualize multiple DNA sequences simultaneously. When a probe comes into contact with DNA on a specific chromosome, hybridization will occur. Consequently, information regarding the location of that sequence of DNA will be attained. FISH analyzes single stranded DNA (ssDNA). Once the DNA is in its single stranded state, the DNA can bind to its specific probe.

Horse genome

horse genome project
The horse genome was first sequenced in 2006. The Horse Genome Project mapped 2.7 billion DNA base pairs, and released the full map in 2009. The horse genome is larger than the dog genome, but smaller than the human genome or the bovine genome. It encompasses 31 autosomes and two sex chromosomes. As horses share over 90 hereditary diseases similar to those found in humans, the sequencing of the horse genome has potential applications to both equine and human health. Further, nearly half of the chromosomes in the horse genome show conserved synteny with a human chromosome, far more than between dogs and humans.

Oryzomys

rice ratsOryzomys sp. n.rice rat
Within Oryzomyini, a 2006 phylogenetic analysis by Marcelo Weksler which used both morphological and DNA sequence data found some evidence that Oryzomys is most closely related to a group including Holochilus, Lundomys, and Pseudoryzomys. Although analyses based on morphological and combined data supported this relationship, sequences of the Rbp3 gene alone instead placed Oryzomys among a group that included Nectomys, Sigmodontomys, and a few other genera. In all analyses, Oryzomys appeared within clade D of Oryzomyini.

Fungus

Fungifungalnecrotrophic
Advances in molecular genetics have opened the way for DNA analysis to be incorporated into taxonomy, which has sometimes challenged the historical groupings based on morphology and other traits. Phylogenetic studies published in the last decade have helped reshape the classification within Kingdom Fungi, which is divided into one subkingdom, seven phyla, and ten subphyla. The English word fungus is directly adopted from the Latin fungus (mushroom), used in the writings of Horace and Pliny.

Helix (genomics company)

Helix
Helix handles sample collection, DNA sequencing, and secure data storage and partners develop on-demand products. Helix is headquartered in the San Francisco Bay Area and operates a sequencing laboratory in San Diego. In 2016, Helix partnered with the National Geographic Society to sequence DNA for the Genographic Project. In 2018, Helix partnered with the Desert Research Institute and Renown Institute of Health Innovation in support of the Healthy Nevada project, which offers free access to genomic sequencing to 40,000 residents of northern Nevada for health research.

Cloning

cloneclonescloned
In practice, localization of the gene to a chromosome or genomic region does not necessarily enable one to isolate or amplify the relevant genomic sequence. To amplify any DNA sequence in a living organism, that sequence must be linked to an origin of replication, which is a sequence of DNA capable of directing the propagation of itself and any linked sequence. However, a number of other features are needed, and a variety of specialised cloning vectors (small piece of DNA into which a foreign DNA fragment can be inserted) exist that allow protein production, affinity tagging, single stranded RNA or DNA production and a host of other molecular biology tools.

Transandinomys talamancae

Talamancan rice ratT. talamancae
In 2006, Marcelo Weksler published a phylogenetic analysis of Oryzomyini ("rice rats"), the tribe to which Oryzomys is allocated, using morphological data and DNA sequences from the IRBP gene. His results showed species of Oryzomys dispersed across Oryzomyini and suggested that most species in the genus should be allocated to new genera. Oryzomys talamancae was also included; it appeared within "clade B", together with other species formerly associated with Oryzomys capito. Some analyses placed it closest to species now placed in Euryoryzomys or Nephelomys, but with low support.

Oligonucleotide

oligonucleotidesoligoantisense oligonucleotide
Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, library construction and as molecular probes.

Quantitative trait locus

quantitative trait lociQTLQTL mapping
Once a region of DNA is identified as contributing to a phenotype, it can be sequenced. The DNA sequence of any genes in this region can then be compared to a database of DNA for genes whose function is already known, being this task fundamental for marker-assisted crop improvement. Mendelian inheritance was rediscovered at the beginning of the 20th century. As Mendel's ideas spread, geneticists began to connect Mendel's rules of inheritance of single factors to Darwinian evolution. For early geneticists, it was not immediately clear that the smooth variation in traits like body size (i.e., Incomplete Dominance) was caused by the inheritance of single genetic factors.

Mutalyzer

Mutalyzer is a web-based software tool which was primarily developed to check the description of sequence variants identified in a gene during genetic testing. Mutalyzer applies the rules of the standard human sequence variant nomenclature and can correct descriptions accordingly. Apart from the sequence variant description, Mutalyzer requires a DNA sequence record containing the transcript and protein feature annotation as a reference. Mutalyzer 2 accepts GenBank and Locus Reference Genomic (LRG) records. The annotation is also used to apply the correct codon translation tables and generate DNA and protein variant descriptions for any organism.

Accipitridae

accipitridaccipitridshawks
The accipitrids are recognizable by a peculiar rearrangement of their chromosomes. Apart from this, morphology and mtDNA cytochrome b sequence data give a confusing picture of these birds' interrelationships. What can be said is that the hawks, kites, eagles and Old World vultures as presently assigned in all likelihood do not form monophyletic groups: According to the molecular data, the Buteoninae are most likely poly- or paraphyletic, with the true eagles, the sea eagles, and the buteonine hawks apparently representing distinct lineages.

LIANTI

To analyze or sequence very small amount of DNA, i.e. genomic DNA from a single cell, the picograms of DNA is subject to WGA to amplify at least thousands of times into nanogram scale, before DNA analysis or sequencing can be carried out. Previous WGA methods (DOP-PCR, MDA, MALBAC ) use exponential/nonlinear amplification schemes, leading to bias accumulation and error propagation. LIANTI achieved linear amplification of the whole genome for the first time, enabling more uniform and accurate amplification.

Microfluidic whole genome haplotyping

microfluidics
As methods for amplification of small amounts of DNA improve, single chromosome sequencing is possible using microfluidics to separate each individual chromosome. A cost-effective approach may be to barcode each individual chromosome and perform parallel resequencing of the entire individual genome. The amplification of each chromosome separately also provides a mechanism to potentially fill in some of the gaps that remain in the human reference genome. Single chromosome sequencing will allow for unmapped sequences to be associated with a single chromosome.

Mir-16 microRNA precursor family

miR-16miR-16-1
More recently, there is evidence that in colorectal cancer that the efficacy of treatment with the monoclonal antibody cetuximab can be assessed by the expression pattern of colorectal carcinoma after therapy. miR-16 and miR-15a are clustered within a 0.5 kbp region in Chromosome 13 (13q14) in humans, a chromosomal region shown to be deleted or down-regulated in approximately more than half of B-CLL, the most prevalent form of leukemia in adults. Carcinogenesis is a gradual process, involving multiple genetic mutations, thus every patient with malignancy presents with a heterogeneous population of cells.

Folliculin

FLCN
Most mutations are identified by DNA sequencing. With the advent of multiplex ligation-dependent probe amplification (MLPA) technology, partial deletions of the FLCN gene have also been identified permitting a FLCN mutation detection rate in BHD cohorts that approaches 90%. Very few FLCN mutations have been found in association with sporadic kidney tumors indicating that FLCN mutation may play only a minor role in non-inherited kidney cancer. Experimental evidence supports a role for FLCN as a tumor suppressor gene.

Dodo

Raphus cucullatusdodo birdRaphus
Osteological and DNA analysis has since led to the dissolution of the family Raphidae, and the dodo and solitaire are now placed in their own subfamily, Raphinae, within the family Columbidae. In 2002, American geneticist Beth Shapiro and colleagues analysed the DNA of the dodo for the first time. Comparison of mitochondrial cytochrome b and 12S rRNA sequences isolated from a tarsal of the Oxford specimen and a femur of a Rodrigues solitaire confirmed their close relationship and their placement within the Columbidae.

Transposable element

transposontransposable elementstransposons
Repbase – a database of transposable element sequences. RepeatMasker – a computer program used by computational biologists to annotate transposons in DNA sequences. Use of the Sleeping Beauty Transposon System for Stable Gene Expression in Mouse Embryonic Stem Cells.

Melanoma

malignant melanomametastatic melanomamelanomas
Errors in DNA repair of UV photoproducts, or inaccurate synthesis past these photoproducts, can also lead to deletions, insertions and chromosomal translocations. The entire genomes of 25 melanomas were sequenced. On average, about 80,000 mutated bases (mostly C>T transitions) and about 100 structural rearrangements were found per melanoma genome. This is much higher than the approximately 70 mutations across generations (parent to child). Among the 25 melanomas, about 6,000 protein-coding genes had missense, nonsense, or splice site mutations. The transcriptomes of over 100 melanomas has also been sequenced and analyzed.