Usually refers to high-throughput, next-generation sequencing methods, although can also refer to traditional capillary-based Sanger sequencing. Advantages: a lot of data at little cost. Disadvantages: short read length; high error rates. Next-Gen Sequencing is currently the most popular method for generating genetic data in general, and for detecting both single-nucleotide and structural variation.

The use of dense arrays of oligonucleotides deposited on glass slides, subjected to fluorescent Comparative Genomic Hybridization. Probe Intensity Analysis (see Analysis Types below) use test:reference ratios to detect copy number changes. Advantages: one can "scan" an entire genome very rapidly; high sensitivity. Disadvantages: cannot detect inversions or complex rearrangements; cannot determine genomic location of copy number gains (and in some cases losses); resolution not as high as sequencing. Another very popular method for detecting structural variation.

Originally designed to genotype single nucleotide variation in a massively parallel manner, SNP arrays have many of the same advantages and disadvantages as oligonucleotide arrays. However, they have the added benefit of enabling statistical analysis of allelic inhertance patterns between samples from related individuals, thus adding to their ability to detect and describe de novo structural variation events.

BAC arrays pre-date oligo arrays and use as probes replicated bacterial artificial chromosome DNA (average insert length ~150 kilobases) and comparative genomic hybridization between a reference and a test sample. Disadvantages: labor-intensive to produce; very low resolution. Not typically in current use.

The manual aggregation and curation of independently reported structural variants from several online resources. These often clinically important variants would not otherwise find their way into a public catalogue of important structural variation. Examples include variants sporadically reported in the scientific literature, or stored in clinically-oriented online resources (e.g., OMIM) or in locus-specific databases (LSDBs).

The use of microfluidics and highly parallel real-time PCR to digitally count copy number in a sample. Similarly to other array-based techniques, uses comparative genomic hybridization. Rarely used, usually as a validation method.

The use of multiple, differentially colored fluorescently-labeled probes (usu. fosmids, cosmids, or BACs) hybridized to a chromosome spread to detect copy number and position of target loci. Advantages: gives unambiuous relative positional information, can detect balanced and unbalanced translocations. Disadvantages: very low resolution, low throughput, labor intensive.

Similar to other array-based methods, except probes represent transcribed regions rather than the entire genome; therefore, subsequent intensity analysis reflects changes in gene expression which do not necessarily reflect changes in genomic DNA. Advantages: good for identifying possible gene deletions as a by-product of a gene expression experiment. Disadvantages: reduction or loss of signal does not necessarily indicate gene deletion - results must be followed up with more experiments.

May refer to any of several methods involving preparation of chromosome spreads and capable of detecting cytogenetic changes under a microscope. Examples are G-banding and fluorescence-based FISH, or chromosome "painting."

Multiplex Amplifiable Probe Hybridization; based on the quantitative recovery of short amplifiable probes after hybridization to genomic DNA. Advantages: good at detecting specific deletions in clinical samples; potential for high throughput. Rarely used.

MALDI-TOF mass spectroscopy of allele-specific primer extension products. Can be used to determine allele dosage ratios at specific loci in samples with heterozygous genotypes. Used rarely, as a validation method.

Fosmids or other library inserts are fully digested with multiple restriction enzymes, and the resulting restriction pattern is compared to what is expected based on a reference. Used rarely, as a validation method.

Multiplex Ligation-dependent Probe Amplification; fluorescence- and capillary-based detection of copy number changes at specific loci using multiplex PCR. Advantages: low cost; not labor-intensive; excellent for detecting specific small copy number changes like exon duplications and deletions.

An integrated set of methods and analyses which involve stretching DNA into a single filament, immobilizing it on a charged surface, complete digestion with a single restriction enzyme, optical observation of the resulting restriction pattern, and comparison of results against the expected restriction pattern based on a reference genome. Advantages: ability to detect location and nature of insertions, deletions, and inversions. Disadvantages: highly specialized; cannot alone determine the sequence content or genomic origin of abberant events.

The use of polymerase chain reaction technology to determine the presence or absence of a specified genomic locus. Advantages: easy; quick; inexpensive. Disadvantages: low throughput; low resolution. Typically used to genotype specific loci of interest.

Similar to PCR but fluorescence-based and able to detect copy number with some degree of accuracy.

Representational Oligonucleotide Microarray Analysis. Same as oligo aCGH except restriction digest and PCR amplification are applied to samples to reduce genomic complexity and thereby increase hybridization efficiency.