Shapiro–Senapathy algorithm

[1] Using a weighted table of nucleotide frequencies, the S&S algorithm outputs a consensus-based percentage for the possibility of the window containing a splice site.

The mutations in the donor and acceptor splice sites in different genes causing a variety of cancers that have been identified by S&S are shown in Table 1.

A few example mutations in the donor and acceptor splice sites in different genes causing a variety of inherited disorders identified using S&S are shown in Table 2. causing a truncated protein[55] site 17 nt upstream in the exon[56] stop codon will produce a truncated protein lacking the binding sites for myosin and titin[57] More than 100 immune system disorders affect humans, including inflammatory bowel diseases, multiple sclerosis, systemic lupus erythematosus, bloom syndrome, familial cold autoinflammatory syndrome, and dyskeratosis congenita.

The Shapiro–Senapathy algorithm has been used to discover genes and mutations involved in many immune disorder diseases, including Ataxia telangiectasia, B-cell defects, epidermolysis bullosa, and X-linked agammaglobulinemia.

Xeroderma pigmentosum, an autosomal recessive disorder is caused by faulty proteins formed due to new preferred splice donor site identified using S&S algorithm and resulted in defective nucleotide excision repair.

[61] Identification of Familial tumoral calcinosis (FTC) is an autosomal recessive disorder characterized by ectopic calcifications and elevated serum phosphate levels and it is because of aberrant splicing.

[62] Applying the S&S technology platform in modern clinical genomics research hasadvance diagnosis and treatment of human diseases.

This method for detecting deleterious splicing mutations in eukaryotic genes has been used extensively in disease research in the humans, animals and plants over the past three decades, as described above.

These methods also formed the basis of all subsequent tools development for discovering genes in uncharacterized genomic sequences.

The S&S has thus paved the way to determine the mechanisms by which a deleterious mutation could lead to a defective protein, resulting in different diseases depending on which gene is affected.

[88] The splicing and exon–intron junction prediction coincided with the GT/AG rule (S&S) in the Molecular characterization and evolution of carnivorous sundew (Drosera rotundifolia L.) class V b-1,3-glucanase.

[89] Unspliced (LSDH) and spliced (SSDH) transcripts of NAD+ dependent sorbitol dehydroge nase (NADSDH) of strawberry (Fragaria ananassa Duch., cv.

[84] Diminution of rbm24a or rbm24b gene products by morpholino knockdown resulted in significant disruption of somite formation in mouse and zebrafish.

The different types of splicing mutations in genes. Mutations within the splicing regions of genes can lead to a defective transcript and protein. Depending on where exactly the mutation occurs and which "cryptic" splice site near the original site is chosen for splicing, the specific defect in the transcript and protein will vary. Frequently, splicing mutations will lead to exon skipping, intron inclusion, exon extension/truncation, and premature termination in the resulting transcript. The various defects in the transcript will in turn result in different kinds of disruption in the amino acid sequence of the protein.
ExampleofColorectalCancer
Exon Skipping caused by a donor mutation in the gene MLH1 leading to colorectal cancer . The generation of a mRNA from a split gene involves the transcription of the gene into the primary RNA transcript, and the precise removal of the introns and the joining of the exons from the primary RNA transcript. A deleterious mutation within the splicing signals (donor or acceptor splice sites) can affect the recognition of the correct splice junction and lead to an aberration in the joining of the authentic exons. Depending on if the mutation occurs within the donor or the acceptor site, and the particular base that is mutated within the splice sequence, the aberration could lead to the skipping of a complete or partial exon, or the inclusion of a partial intron or a cryptic exon in the mRNA produced by the splicing process. Either of these situations will usually lead to a premature stop codon in the mRNA and result in a completely defective protein. The S&S algorithm aids in determining which splice site and exon in a gene are mutated, and the S&S score of the mutated splice site aids in determining the type of splicing aberration and the resulting mRNA structure and sequence. The example gene MLH1 affected in colorectal cancer is shown in the figure. It was found using the S&S algorithm that a mutation in the donor splice site in exon 8 led to the skipping of the exon 8. The mRNA thus lacks the sequence corresponding to exon 8 (sequence positions are shown in the figure). This causes a frame shift in the mRNA coding sequence at amino acid position 226, leading to premature protein truncation at amino acid position 233. This mutated protein is completely defective, which has led to colorectal cancer in the patient.