Jan Schouten (geneticist)

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Johannes Petrus Schouten (born 17 May 1956, in Schoorl) is a Dutch scientist, entrepreneur and philanthropist. [1] He is the inventor of Multiplex-Ligation-dependent Probe Amplification (MLPA), a method for the research of genetic disorders. [2] [3] [4] [5] He founded the biotech company MRC Holland, based in Amsterdam [6] and the MRC Holland Foundation. [7]

Contents

Early life and education

Schouten was born in Schoorl Noord-Holland. He studied cell biology at Wageningen University. After earning his PhD he became an entrepreneur. [8]

Career

In 1985 he founded the company MRC Holland, which was based in the buildings of the Vrije Universiteit in Amsterdam. The company first focused on the production of restriction enzymes. [6] In 2002, Schouten invented MLPA, [2] a method for genetic testing. The method detects copy number variation in genes or parts of genes, an important cause for hereditary disorders or the development of tumours. [9] [10] The method is considered simple, reliable and relatively cheap, and therefore a popular choice in laboratories worldwide, including in developing countries. [11] [10]

In 2019, Schouten was awarded for his work with the Order of the Lion of the Netherlands, a royal distinction that recognizes merit in art and science. [1] [12] [13]

Publications

His most cited papers are

Philanthropy

In 2011, Schouten and his wife started the MRC Holland Foundation whose mission is to improve educational facilities in The Gambia and as such they work closely with the country's Ministry of Education. [15] [1] [16] [17]

Related Research Articles

<span class="mw-page-title-main">Polymerase chain reaction</span> Laboratory technique to multiply a DNA sample for study

The polymerase chain reaction (PCR) is a method widely used to make millions to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA sufficiently to enable detailed study. PCR was invented in 1983 by American biochemist Kary Mullis at Cetus Corporation. Mullis and biochemist Michael Smith, who had developed other essential ways of manipulating DNA, were jointly awarded the Nobel Prize in Chemistry in 1993.

<span class="mw-page-title-main">DNA sequencing</span> Process of determining the nucleic acid sequence

DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.

In molecular biology, a hybridization probe(HP) is a fragment of DNA or RNA of usually 15–10000 nucleotide long which can be radioactively or fluorescently labeled. HP can be used to detect the presence of nucleotide sequences in analyzed RNA or DNA that are complementary to the sequence in the probe. The labeled probe is first denatured (by heating or under alkaline conditions such as exposure to sodium hydroxide) into single stranded DNA (ssDNA) and then hybridized to the target ssDNA (Southern blotting) or RNA (northern blotting) immobilized on a membrane or in situ.

<i>In situ</i> hybridization

In situ hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA, RNA or modified nucleic acids strand to localize a specific DNA or RNA sequence in a portion or section of tissue or if the tissue is small enough, in the entire tissue, in cells, and in circulating tumor cells (CTCs). This is distinct from immunohistochemistry, which usually localizes proteins in tissue sections.

<span class="mw-page-title-main">Real-time polymerase chain reaction</span> Laboratory technique of molecular biology

A real-time polymerase chain reaction is a laboratory technique of molecular biology based on the polymerase chain reaction (PCR). It monitors the amplification of a targeted DNA molecule during the PCR, not at its end, as in conventional PCR. Real-time PCR can be used quantitatively and semi-quantitatively.

<span class="mw-page-title-main">Rolling circle replication</span> DNA synthesis technique

Rolling circle replication (RCR) is a process of unidirectional nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA or RNA, such as plasmids, the genomes of bacteriophages, and the circular RNA genome of viroids. Some eukaryotic viruses also replicate their DNA or RNA via the rolling circle mechanism.

Multiplex ligation-dependent probe amplification (MLPA) is a variation of the multiplex polymerase chain reaction that permits amplification of multiple targets with only a single primer pair. It detects copy number changes at the molecular level, and software programs are used for analysis. Identification of deletions or duplications can indicate pathogenic mutations, thus MLPA is an important diagnostic tool used in clinical pathology laboratories worldwide.

Loop-mediated isothermal amplification (LAMP) is a single-tube technique for the amplification of DNA and a low-cost alternative to detect certain diseases. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) combines LAMP with a reverse transcription step to allow the detection of RNA.

<span class="mw-page-title-main">Nucleic acid test</span> Group of techniques to detect a particular nucleic acid sequence

A nucleic acid test (NAT) is a technique used to detect a particular nucleic acid sequence and thus usually to detect and identify a particular species or subspecies of organism, often a virus or bacterium that acts as a pathogen in blood, tissue, urine, etc. NATs differ from other tests in that they detect genetic materials rather than antigens or antibodies. Detection of genetic materials allows an early diagnosis of a disease because the detection of antigens and/or antibodies requires time for them to start appearing in the bloodstream. Since the amount of a certain genetic material is usually very small, many NATs include a step that amplifies the genetic material—that is, makes many copies of it. Such NATs are called nucleic acid amplification tests (NAATs). There are several ways of amplification, including polymerase chain reaction (PCR), strand displacement assay (SDA), or transcription mediated assay (TMA).

The versatility of polymerase chain reaction (PCR) has led to modifications of the basic protocol being used in a large number of variant techniques designed for various purposes. This article summarizes many of the most common variations currently or formerly used in molecular biology laboratories; familiarity with the fundamental premise by which PCR works and corresponding terms and concepts is necessary for understanding these variant techniques.

The ligase chain reaction (LCR) is a method of DNA amplification. The ligase chain reaction (LCR) is an amplification process that differs from PCR in that it involves a thermostable ligase to join two probes or other molecules together which can then be amplified by standard polymerase chain reaction (PCR) cycling. Each cycle results in a doubling of the target nucleic acid molecule. A key advantage of LCR is greater specificity as compared to PCR. Thus, LCR requires two completely different enzymes to operate properly: ligase, to join probe molecules together, and a thermostable polymerase to amplify those molecules involved in successful ligation. The probes involved in the ligation are designed such that the 5′ end of one probe is directly adjacent to the 3′ end of the other probe, thereby providing the requisite 3′-OH and 5′-PO4 group substrates for the ligase.

OLIGO Primer Analysis Software is a software for DNA primer design. The first paper describing this software was published in 1989. The program is a real time PCR primer and probe search and analysis tool, in addition to siRNA and molecular beacon searches, open reading frame, restriction enzyme analysis. It was created and maintained by Wojciech Rychlik and Piotr Rychlik.

Multiplex polymerase chain reaction refers to the use of polymerase chain reaction to amplify several different DNA sequences simultaneously. This process amplifies DNA in samples using multiple primers and a temperature-mediated DNA polymerase in a thermal cycler. The primer design for all primers pairs has to be optimized so that all primer pairs can work at the same annealing temperature during PCR.

Molecular Inversion Probe (MIP) belongs to the class of Capture by Circularization molecular techniques for performing genomic partitioning, a process through which one captures and enriches specific regions of the genome. Probes used in this technique are single stranded DNA molecules and, similar to other genomic partitioning techniques, contain sequences that are complementary to the target in the genome; these probes hybridize to and capture the genomic target. MIP stands unique from other genomic partitioning strategies in that MIP probes share the common design of two genomic target complementary segments separated by a linker region. With this design, when the probe hybridizes to the target, it undergoes an inversion in configuration and circularizes. Specifically, the two target complementary regions at the 5’ and 3’ ends of the probe become adjacent to one another while the internal linker region forms a free hanging loop. The technology has been used extensively in the HapMap project for large-scale SNP genotyping as well as for studying gene copy alterations and characteristics of specific genomic loci to identify biomarkers for different diseases such as cancer. Key strengths of the MIP technology include its high specificity to the target and its scalability for high-throughput, multiplexed analyses where tens of thousands of genomic loci are assayed simultaneously.

9q34 deletion syndrome is a rare genetic disorder. Terminal deletions of chromosome 9q34 have been associated with childhood hypotonia, a distinctive facial appearance and developmental disability. The facial features typically described include arched eyebrows, small head circumference, midface hypoplasia, prominent jaw and a pouting lower lip. Individuals with this disease may often have speech impediments, such as speech delays. Other characteristics of this disease include: epilepsy, congenital and urogenital defects, microcephaly, corpulence, and psychiatric disorders. From analysis of chromosomal breakpoints, as well as gene sequencing in suggestive cases, Kleefstra and colleagues identified EHMT1 as the causative gene. This gene is responsible for producing the protein histone methyltransferase which functions to alter histones. Ultimately, histone methyltransferases are important in deactivating certain genes, needed for proper growth and development. Moreover, a frameshift, missense, or nonsense error in the coding sequence of EHMT1 can result in this condition in an individual.

Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged between 1993 and 1998 and have been commercially available since 2005. These technologies use miniaturized and parallelized platforms for sequencing of 1 million to 43 billion short reads per instrument run.

Nablus mask-like facial syndrome is a rare genetic condition. It is a microdeletion syndrome triggered by a deletion at chromosome 8 q22.1 that causes a mask-like facial appearance in those affected. This syndrome typically presents itself in infants, specifically newborns.

<span class="mw-page-title-main">Ligation (molecular biology)</span>

Ligation is the joining of two nucleic acid fragments through the action of an enzyme. It is an essential laboratory procedure in the molecular cloning of DNA, whereby DNA fragments are joined to create recombinant DNA molecules (such as when a foreign DNA fragment is inserted into a plasmid). The ends of DNA fragments are joined by the formation of phosphodiester bonds between the 3'-hydroxyl of one DNA terminus with the 5'-phosphoryl of another. RNA may also be ligated similarly. A co-factor is generally involved in the reaction, and this is usually ATP or NAD+. Eukaryotic cells ligases belong to ATP type, and NAD+ - dependent are found in bacteria (e.g. E. coli).

<span class="mw-page-title-main">Spatial transcriptomics</span> Range of methods designed for assigning cell types

Spatial transcriptomics is a method for assigning cell types to their locations in the histological sections and can also be used to determine subcellular localization of mRNA molecules. First described in 2016 by Ståhl et al., it has since undergone a variety of improvements and modifications.

The proximity extension assay (PEA) is a method for detecting and quantifying the amount of many specific proteins present in a biological sample such a serum or plasma. The method is used in the research field of proteomics, specifically affinity proteomics, where in one searches for differences in the abundance of many specific proteins in blood for use as a biomarker. Biomarkers and biomarker signature combinations, are useful for determining disease states and drug efficacy. Most methods for detecting proteins involve the use of a solid phase for first capturing and immobilizing the protein analyte, where in one or a few proteins are quantified, such as ELISA. In contrast, PEA is performed without a solid phase in a homogeneous one tube reaction solution where in sets of antibodies coupled to unique DNA sequence tags, so called proximity probes, work in pairs specific for each target protein. PEA is often performed using antibodies and is a type of immunoassay. Target binding by the proximity probes increases their local relative effective concentration of the DNA-tags enabling hybridization of weak complementarity to each other which then enables a DNA polymerase mediated extension forming a united DNA sequence specific for each target protein detected. The use of 3'exonuclease proficient polymerases lowers background noise and hyper thermostable polymerases mediate a simple assay with a natural hot-start reaction. This created pool of extension products of DNA sequence forms amplicons amplified by PCR where each amplicon sequence corresponds to a target proteins identity and the amount reflects its quantity. Subsequently, these amplicons are detected and quantified by either real-time PCR or next generation DNA sequencing by DNA-tag counting. PEA enables the detection of many proteins simultaneously due to the readout requiring the combination of two correctly bound antibodies per protein to generate a detectable DNA sequence from the extension reaction. Only cognate pairs of sequence are detected as true signal, enabling multiplexing beyond solid phase capture methods limited at around 30 proteins at a time. The DNA amplification power also enable minute sample volumes even below one microliter. PEA has been used in over 1000 research publications.

References

  1. 1 2 3 Parool, Het (2019-03-17). "Echtpaar onderscheiden voor ontwikkeling gezondheidszorg". Het Parool (in Dutch). Retrieved 2021-05-14.
  2. 1 2 Schouten, JP; McElgunn, CJ; Waaijer, R; Zwijnenburg; Diepvens, F; Pals, G (June 2002). "Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification". Nucleic Acids Research. 30 (12): e57. doi: 10.1093/nar/gnf056 . ISSN   1362-4962. PMC   117299 . PMID   12060695.
  3. ↑ EP 1255871,Schouten, Johannes Petrus,"Multiplex ligatable probe amplification",issued 2001-02-15
  4. ↑ "Multiplex Ligation-dependent Probe Amplification (MLPA)". Bitesize Bio. 2018-12-27. Retrieved 2021-05-21.
  5. ↑ "BMedia - Wetenschapsjournalistiek". www.bmedia.nl. Retrieved 2021-05-21.
  6. 1 2 "About MRC Holland - MRC Holland". www.mrcholland.com. Retrieved 2021-05-14.
  7. ↑ "MRC Holland Foundation". Heroes Awards. 2020-03-02. Retrieved 2021-05-14.
  8. ↑ "Kennisuitwisseling" (PDF).
  9. ↑ Stuppia, L; Antonucci, I; Palka, G; Gatta, V (March 2012). "Use of the MLPA Assay in the Molecular Diagnosis of Gene Copy Number Alterations in Human Genetic Diseases". International Journal of Molecular Sciences. 13 (3): 3245–76. doi: 10.3390/ijms13033245 . ISSN   1422-0067. PMC   3317712 . PMID   22489151.
  10. 1 2 Vorstman, JS; Jalali, GR; Rappaport, EF; Hacker, AM; Scott, C; Emanuel, BS (August 2006). "MLPA: a rapid, reliable, and sensitive method for detection and analysis of abnormalities of 22q". Human Mutation. 27 (8): 14–821. doi:10.1002/humu.20330. ISSN   1098-1004. PMC   2814414 . PMID   16791841.
  11. ↑ Jehee, Fernanda Sarquis; Takamori, Jean Tetsuo; Medeiros, Paula F. Vasconcelos; Pordeus, Ana Carolina B.; Latini, Flavia Roche M.; Bertola, Débora Romeo; Kim, Chong Ae; Passos-Bueno, Maria Rita (July 2011). "Using a combination of MLPA kits to detect chromosomal imbalances in patients with multiple congenital anomalies and mental retardation is a valuable choice for developing countries". European Journal of Medical Genetics. 54 (4): e425–432. doi: 10.1016/j.ejmg.2011.03.007 . ISSN   1878-0849. PMID   21457803.
  12. ↑ "Koninklijke onderscheiding voor echtpaar dat bijdraagt aan de ontwikkeling van de gezondheidszorg". www.amsterdamsdagblad.nl/ (in Dutch). Retrieved 2021-05-14.
  13. ↑ Twitter https://twitter.com/amsterdamnl/status/1106580730958745609 . Retrieved 2021-05-21.{{cite web}}: Missing or empty |title= (help)
  14. 1 2 3 4 Google Scholar Author page, Accessed May 21, 2021
  15. ↑ "MRC Holland Foundation - MRC Holland". www.mrcholland.com. Retrieved 2021-05-14.
  16. ↑ "MRC-Holland Foundation" (in Dutch). Retrieved 2021-05-14.
  17. ↑ MRC Holland Foundation Documentary Part 1 , retrieved 2021-05-14
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