20. FISH

FISH will detect a specific chromosomal anomaly that has been previously suspected. In prenatal diagnosis typically abnormality of chromosome 21, 13, 18, X, Y. It gives results between 72 h. For example if the triple markers in maternal serum and first trimester are suggesting Down's syndrome, a specific FISH for chromosome 21 can be performed. But if there is no specific suspicion it is better to do karyotyping.

A FISH may detect micro deletions also but it has to be planned which micro deletion we are looking for. For example 22q micro deletions responsible for Di George Syndrome in a cardiac anomaly like tetralogy of Fallot. Laboratories usually have a panel for common micro deletions. 22q micro deletion is the second most common chromosomal anomaly after Trisomy 21.

#### 21. Microarray

Almost all mutations are very small with only 100–1000 pairs. For these we have to depend on cytogenetic tests like Mutation testing (Sanger Sequence), microarray, Exome sequencing and genome sequencing. If we do not know what to test for than we have to order a microarray. It will scan the entire genome if some few hundreds of base pairs are missing or not. For example, microarray gene testing of uterine endometrium in cases of recurrent implantation failure following in vitro fertilization and embryo transfer.

#### 22. Exom and genome sequencing

These are the most precise tests telling us abnormalities in the minute base pairs. These are expensive with last resorts.

An analogy is a library with 23 bookshelves. Each shelf has 10 rows and each row has 25 books. A karyotype is to find if a bookshelf is in excess or missing. Also it can also tell if a major part of bookshelf is broken. A micro deletion is like a missing row in a bookshelf.

A microarray can identify if a book or two is missing in the library but then sometimes it tells a book which is not important. A mutation specific test is like checking if a particular book is missing. For example a book on Indian cooking in a row of cookery books.

An Exom sequencing is like checking if a few pages are missing in any book in any shelf of the whole library. Genome sequencing is like checking if any paragraph or sentence is missing in any book in any shelf in the whole library. Majority of the fetal birth defects are due to single gene/multiple gene mutations and cannot be identified in karyotyping.
