Name: a novel strategy combining array-cgh, whole-exome sequencing and in utero electroporation in rodents to identify causative genes for brain malformations
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Description: Watch this Scientific Journal Video about A Novel Strategy Combining Array-CGH, Whole-exome Sequencing and In Utero Electroporation in Rodents to Identify Causative Genes for Brain Malformations at Jo

We thank Dr. G. McGillivray, Pr. J. Clayton-Smith, Pr. W.B. Dobyns, Pr. P. Striano, Pr. I.E. Scheffer, Pr. S.P. Roberston and Pr. S.F. Berkovic for providing MCD patients. We thank Dr. F. Michel and D. Mei for technical advices and help. This work was supported by funding from the Seven Framework Programme of the EU, DESIRE project, contract number: Health-F2-602531-2013, (to V.C., R.G., A.R., A.F. and C.C.), INSERM (to A.R. and C.C.), Fondation J&#233;r&#244;me Lejeune (R13083AA to A.F, E.P.P and C.C) and R&#233;gion Provence Alpes C&#244;te d&#39;Azur (APO2014 - DEMOTIC to C.C. and A.A.D). D.A.K is an EMBO Young Investigator and is supported by FWF grants (I914 and P24367).

Ethics Statement: Wistar rats were mated, maintained and used in the INMED animal facilities, in agreement with European Union and French legislation.
1. DNA Extraction and Quantification for Array-CGH and WES
<ol>
	<li>Extract Genomic DNA (gDNA) from human blood leukocytes from patients using an automated DNA isolation robot or commercially available manual DNA extraction kits according to the manufacturer&#39;s protocol. Quantify all samples using a spectrophotometer.</li>
</ol>
<p class="...

<ol>
	<li>Meencke, H. J., Veith, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Migration+disturbances+in+epilepsy.">Migration disturbances in epilepsy.</a> Epilepsy Res. 9, 31-39 (1992).</li><li>Shorvon, S., Stefan, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overview+of+the+safety+of+newer+antiepileptic+drugs.">Overview of the safety of newer antiepileptic drugs.</a> Epilepsia. 38 (1), 45-51 (1997).</li><li>Parrini, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Periventricular+heterotopia:+phenotypic+heterogeneity+and+correlation+with+Filamin+A+mutations.">Periventricular heterotopia: phenotypic heterogeneity and correlation with Filamin A mutations.</a> Brain. 129 (7), 1892-1906 (2006).</li><li>Fox, J. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mutations+in+filamin+1+prevent+migration+of+cerebral+cortical+neurons+in+human+periventricular+heterotopia.">Mutations in filamin 1 prevent migration of cerebral cortical neurons in human periventricular heterotopia.</a> Neuron. 21 (6), 1315-1325 (1998).</li><li>Sheen, V. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mutations+in+ARFGEF2+implicate+vesicle+trafficking+in+neural+progenitor+proliferation+and+migration+in+the+human+cerebral+cortex.">Mutations in ARFGEF2 implicate vesicle trafficking in neural progenitor proliferation and migration in the human cerebral cortex.</a> Nat Genet. 36 (1), 69-76 (2004).</li><li>Cappello, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mutations+in+genes+encoding+the+cadherin+receptor-ligand+pair+DCHS1+and+FAT4+disrupt+cerebral+cortical+development.">Mutations in genes encoding the cadherin receptor-ligand pair DCHS1 and FAT4 disrupt cerebral cortical development.</a> Nat Genet. 45 (11), 1300-1308 (2013).</li><li>Moro, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Periventricular+heterotopia+in+fragile+X+syndrome.">Periventricular heterotopia in fragile X syndrome.</a> Neurology. 67 (4), 713-715 (2006).</li><li>Ferland, R. J., Gaitanis, J. N., Apse, K., Tantravahi, U., Walsh, C. A., Sheen, V. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Periventricular+nodular+heterotopia+and+Williams+syndrome.">Periventricular nodular heterotopia and Williams syndrome.</a> Am J Med Genet A. 140 (12), 1305-1311 (2006).</li><li>van Kogelenberg, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Periventricular+heterotopia+in+common+microdeletion+syndromes.">Periventricular heterotopia in common microdeletion syndromes.</a> Mol Syndromol. 1 (1), 35-41 (2010).</li><li>Sheen, V. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Periventricular+heterotopia+associated+with+chromosome+5p+anomalies.">Periventricular heterotopia associated with chromosome 5p anomalies.</a> Neurology. 60 (6), 1033-1036 (2003).</li><li>Neal, J., Apse, K., Sahin, M., Walsh, C. A., Sheen, V. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deletion+of+chromosome+1p36+is+associated+with+periventricular+nodular+heterotopia.">Deletion of chromosome 1p36 is associated with periventricular nodular heterotopia.</a> Am J Med Genet A. 140 (15), 1692-1695 (2006).</li><li>Cardoso, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Periventricular+heterotopia,+mental+retardation,+and+epilepsy+associated+with+5q14.3-q15+deletion.">Periventricular heterotopia, mental retardation, and epilepsy associated with 5q14.3-q15 deletion.</a> Neurology. 72 (9), 784-792 (2009).</li><li>Cellini, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Periventricular+heterotopia+with+white+matter+abnormalities+associated+with+6p25+deletion.">Periventricular heterotopia with white matter abnormalities associated with 6p25 deletion.</a> Am J Med Genet A. 158 (7), 1793-1797 (2006).</li><li>Bertini, V., De Vito, G., Costa, R., Simi, P., Valetto, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolated+6q+terminal+deletions:+an+emerging+new+syndrome.">Isolated 6q terminal deletions: an emerging new syndrome.</a> Am J Med Genet A. 140 (1), 74-81 (2006).</li><li>Dobyns, W. B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Consistent+chromosome+abnormalities+identify+novel+polymicrogyria+loci+in+1p36.3,+2p16.1-p23.1,+4q21.21-q22.1,+6q26-q27,+and+21q2.">Consistent chromosome abnormalities identify novel polymicrogyria loci in 1p36.3, 2p16.1-p23.1, 4q21.21-q22.1, 6q26-q27, and 21q2.</a> Am J Med Genet A. 146 (13), 1637-1654 (2008).</li><li>Conti, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Periventricular+heterotopia+in+6q+terminal+deletion+syndrome:+role+of+the+C6orf70+gene.">Periventricular heterotopia in 6q terminal deletion syndrome: role of the C6orf70 gene.</a> Brain. 136 (11), 3378-3394 (2013).</li><li>Sheen, V. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Etiological+heterogeneity+of+familial+periventricular+heterotopia+and+hydrocephalus.">Etiological heterogeneity of familial periventricular heterotopia and hydrocephalus.</a> Brain Dev. 26 (5), 326-334 (2004).</li><li>Jaglin, X. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mutations+in+the+beta-tubulin+gene+TUBB2B+result+in+asymmetrical+polymicrogyria.">Mutations in the beta-tubulin gene TUBB2B result in asymmetrical polymicrogyria.</a> Nat. Genet. 41 (6), 746-752 (2009).</li><li>Falace, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TBC1D24+regulates+neuronal+migration+and+maturation+through+modulation+of+the+ARF6-dependent+pathway.">TBC1D24 regulates neuronal migration and maturation through modulation of the ARF6-dependent pathway.</a> Proc Natl Acad Sci U S A. 111 (6), 2337-2342 (2014).</li><li>Lunter, G., Goodson, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stampy:+a+statistical+algorithm+for+sensitive+and+fast+mapping+of+Illumina+sequence+reads.">Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.</a> Genome Res. 21 (6), 936-939 (2011).</li><li>Pagnamenta, A. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exome+sequencing+can+detect+pathogenic+mosaic+mutations+present+at+low+allele+frequencies.">Exome sequencing can detect pathogenic mosaic mutations present at low allele frequencies.</a> J Hum Genet. 57 (1), 70-72 (2012).</li><li>Yu, J. Y., DeRuiter, S. L., Turner, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+interference+by+expression+of+short-interfering+RNAs+and+hairpin+RNAs+in+mammalian+cells.">RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells.</a> Proc Natl Acad Sci U S A. 99 (9), 6047-6052 (2002).</li><li>Bai, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNAi+reveals+doublecortin+is+required+for+radial+migration+in+rat+neocortex.">RNAi reveals doublecortin is required for radial migration in rat neocortex.</a> Nat Neurosci. 6 (12), 1277-1283 (2003).</li><li>Carabalona, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+glial+origin+for+periventricular+nodular+heterotopia+caused+by+impaired+expression+of+Filamin-A.">A glial origin for periventricular nodular heterotopia caused by impaired expression of Filamin-A.</a> Hum Mol Genet. 21 (5), 1004-1017 (2012).</li></ol>

MCDs are important causes of intellectual disability and account for 20-40% of drug-resistant childhood epilepsy1,2. Interest in MCDs has increased dramatically over the past decade as a result of two major factors. The first is the improvement in brain imaging (particularly MRI), which allows physicians and scientists to visualize many brain malformations that were not previously recognized. The other is the evolution of genetic tools that have allowed the ident...

The cerebral cortex plays a key role in cognitive and intellectual processes and is involved in emotional control as well as learning and memory. It is therefore not surprising that many neurological and psychiatric diseases result from malformations of cortical development (MCD). The etiology of MCD is complex since both acquired and genetic factors are involved. The cumulative prevalence of genetically determined proportion of MCD is about 2% and they are sporadic in most cases. For instance, the incidence of congenital brain dysgenesis was estimated to be higher than 1% in the human population, and some forms of MCD are observed in more than 14% of all patients with epilepsy and in 40% of severe or intractable epilepsy1,2.
Periventricular Nodular Heterotopia (PNH) is one of the most common MCDs and is caused by abnormal migration of neurons from the ventricular zone (VZ) to the developing cerebral cortex. The failure of neurons to migrate results in clusters of heterotopic neurons along the walls of the lateral ventricles which can usually be visualized using Magnetic Resonance Imaging (MRI). The clinical, anatomic and imaging features of PNH are heterogeneous. Nodules may range from small and unilateral to bilateral and symmetric. Common clinical sequelae include epilepsy and intellectual disabilities3. Mutations in the Filamin A (or FLNA) gene, which maps in Xq28, were found in 100% of families with X-linked bilateral PNH and in 26% of sporadic patients3,4. A rare, recessive form of PNH caused by mutations in the ARFGEF2 gene, which maps in 20q13, has been reported in two consanguineous families5. Recently, biallelic mutations in genes encoding the receptor-ligand cadherin pair DCHS1 and FAT4 have been identified in nine patients affected by a multisystemic disorder that includes PNH6. PNH has also been associated with fragile X syndrome7, Williams syndrome8, 22q11 microdeletion syndrome9, duplications at 5p1510, deletions at 1p3611, 5q14.3-q1512, 6p2513 and 6q terminal deletion syndrome14,15,16,17,18,19, suggesting that additional causative genes are scattered throughout the genome. However, for approximately 74% of sporadic PNH patients the genetic basis remains to be elucidated17.
Classical gene mapping approaches such as array Comparative Genomic Hybridization (array-CGH) have proven to be a powerful tools for the detection of sub-microscopic chromosomal abnormalities, however, the genomic regions identified using this approach are often large and contain numerous genes.
The advent of massive parallel sequencing techniques (i.e. Whole-Exome Sequencing (WES) and Whole-Genome sequencing (WGS)) has substantially reduced both the cost and the time required to sequence an entire human exome or genome. Nevertheless, interpretation of WES and WGS data remains challenging in the majority of cases, since for each patient tens to hundreds (or even thousands, depending from the type of analysis) variants emerge from data filtering.
To speed up the process of identifying novel MCD causative genes, a novel systematic strategy combining array-CGH, WES and in utero electroporation (IUE) screening of candidate genes was designed. IUE allows to selectively inactivate (or overexpress) specific genes or mutations in rodent brains, enabling rapid evaluation of their involvement in corticogenesis18,19. RNAi mediated-knockdown or overexpression of one or more candidate genes is expected to cause, when the gene is associated with disease development, localized defects in neuronal migration and/or maturation. Upon the identification of a gene whose inactivation (or overexpression) reproduces the phenotype observed in patients in rodents, it becomes an outstanding candidate for the screening in sporadic patients with MCD. Using this approach, we recently revealed the crucial contribution of the C6orf70 gene (also known as ERMARD) in PNH pathogenesis in patients harbouring 6q27 chromosomal deletions16.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr >
			<td >Picospritzer III</td>
			<td >Parker Hannifin Corp</td>
			<td >P/N 051-0500-900</td>
			<td >Intracellular Microinjection Dispense Systems</td>
		</tr>
		<tr >
			<td >Fast Green FCF</td>
			<td >Sigma-Aldrich</td>
			<td >F7252</td>
			<td>Fast green allow visual monitoring of the injection</td>
		</tr>
		<tr >
			<td >BTX ECM 830 electroporator</td>
			<td >BTX Harvard Apparatus</td>
			<td >45-0002</td>
			<td>The ECM 830 is a Square Wave Pulse generator designed for in vitro and in vivo applications</td>
		</tr>
		<tr >
			<td >Microtome HM 650 V</td>
			<td >Microm</td>
			<td>10076838</td>
			<td>Microtome HM 650 V vibratome 240V 50/60Hz with vibrating blade</td>
		</tr>
		<tr >
			<td >FluoView 300</td>
			<td >Olympus</td>
			<td ></td>
			<td>The Olympus FluoViewTM 300 is a point-scanning, point-detection, confocal laser scanning microscope designed for biology research application</td>
		</tr>
		<tr >
			<td >eCELLence software</td>
			<td >Glance Vision Technologies</td>
			<td ></td>
			<td>eCELLence is software designed for the quantitive analysis of cell migration</td>
		</tr>
		<tr >
			<td >Agilent Microarray Scanner Bundle</td>
			<td ></td>
			<td ></td>
			<td>Array slides</td>
		</tr>
		<tr >
			<td >for 1 x 244K, 2 x 105K, 4 x 44K or 8 x 15K</td>
			<td >Agilent</td>
			<td >Agilent p/n G4900DA, G2565CA or G2565BA</td>
			<td ></td>
		</tr>
		<tr >
			<td >for 1 x 1M, 2 x 400K, 4 x 180K or 8 x 60K</td>
			<td >Agilent</td>
			<td >Agilent p/n G4900DA or G2565CA</td>
			<td ></td>
		</tr>
		<tr >
			<td >Hybridization Chamber, stainless</td>
			<td >Agilent</td>
			<td>Agilent p/n G2534A</td>
			<td>Chamber for array CGH hybridization</td>
		</tr>
		<tr >
			<td >Hybridization Chamber gasket slides, 5-pack</td>
			<td></td>
			<td ></td>
			<td>Gasket for array CGH hybridization</td>
		</tr>
		<tr >
			<td >for 1-pack microarrays or</td>
			<td >Agilent</td>
			<td >Agilent p/n G2534-60003</td>
			<td></td>
		</tr>
		<tr >
			<td >for 2-pack microarrays or</td>
			<td >Agilent</td>
			<td >Agilent p/n G2534-60002</td>
			<td></td>
		</tr>
		<tr >
			<td >for 4-pack microarrays or</td>
			<td >Agilent</td>
			<td >Agilent p/n G2534-60011</td>
			<td></td>
		</tr>
		<tr >
			<td >for 8-pack microarrays</td>
			<td >Agilent</td>
			<td >Agilent p/n G2534-60014</td>
			<td></td>
		</tr>
		<tr >
			<td >Hybridization oven</td>
			<td >Agilent</td>
			<td >Agilent p/n G2545A</td>
			<td></td>
		</tr>
		<tr >
			<td >Hybridization oven rotator for Agilent Microarray Hybridization Chambers</td>
			<td >Agilent</td>
			<td >Agilent p/n G2530-60029</td>
			<td></td>
		</tr>
		<tr >
			<td >Thermal cycler with heated lid</td>
			<td >Agilent</td>
			<td >Agilent p/n G8800A or equivalent</td>
			<td>Termal cycler for incubations</td>
		</tr>
		<tr >
			<td >1.5 mL RNase-free Microfuge Tube</td>
			<td >Ambion</td>
			<td >p/n AM12400 or equivalent</td>
			<td>Microcentrifuge</td>
		</tr>
		<tr >
			<td >Magnetic stir bar</td>
			<td >Corning</td>
			<td >p/n 401435 or equivalent</td>
			<td>Instrument for stirring</td>
		</tr>
		<tr >
			<td >Qubit Fluorometer</td>
			<td >Life Technologies</td>
			<td >p/n Q32857</td>
			<td>Instrument for DNA quantification</td>
		</tr>
		<tr >
			<td >Qubit dsDNA BR Assay Kit, for use with the Qubit fluorometer</td>
			<td >Invitrogen</td>
			<td >p/n Q32850</td>
			<td>Kit for Qubit fluorometer</td>
		</tr>
		<tr >
			<td >UV-VIS spectrophotometer</td>
			<td >Thermo Scientific</td>
			<td >NanoDrop 8000 or 2000, or equivalent</td>
			<td>Instrument for DNA quantification</td>
		</tr>
		<tr >
			<td >P10, P20, P200 and P1000 pipettes</td>
			<td >Pipetman or equivalent</td>
			<td ></td>
			<td>DNA dispensation</td>
		</tr>
		<tr >
			<td >Vacuum Concentrator</td>
			<td >Thermo Scientific</td>
			<td >p/n DNA120-115 or 
			equivalent</td>
			<td>Instrument to concentrate DNA</td>
		</tr>
		<tr >
			<td >SureTag Complete DNA Labeling Kit</td>
			<td >Agilent</td>
			<td >p/n 5190-4240</td>
			<td>DNA Labeling Kit (for Human Samples)</td>
		</tr>
		<tr >
			<td >Purification Columns (50 units)</td>
			<td >Agilent</td>
			<td >p/n 5190-3391</td>
			<td>DNA Labeling Kit (for Human Samples)</td>
		</tr>
		<tr >
			<td >AutoScreen A, 96-well plates</td>
			<td >GE Healthcare</td>
			<td >p/n 25-9005-98</td>
			<td>DNA Labeling Kit (for Human Samples)</td>
		</tr>
		<tr >
			<td >GenElute PCR Clean-Up Kit</td>
			<td >Sigma-Aldrich</td>
			<td >p/n NA1020</td>
			<td>DNA Labeling Kit (for Human Samples)</td>
		</tr>
		<tr >
			<td >Human Genomic DNA</td>
			<td ></td>
			<td >p/n G1521</td>
			<td>DNA Labeling Kit (for Human Samples)</td>
		</tr>
		<tr >
			<td >For CGH microarrays:</td>
			<td >Promega</td>
			<td >(female) or p/n G1471 (male)</td>
			<td>Array CGH control DNA</td>
		</tr>
		<tr >
			<td >For CGH+SNP microarrays:</td>
			<td >Coriell</td>
			<td >p/n NA18507, NA18517, NA12891, NA12878, or NA18579</td>
			<td>Array CGH control DNA</td>
		</tr>
		<tr >
			<td >Oligo aCGH/ChIP-on-chip Wash Buffer Kit or</td>
			<td >Agilent</td>
			<td >p/n 5188-5226</td>
			<td>Array CGH hybridization and wash</td>
		</tr>
		<tr >
			<td >Oligo aCGH/ChIP-on-chip Wash Buffer 1 and</td>
			<td >Agilent</td>
			<td >p/n 5188-5221</td>
			<td>Array CGH hybridization and wash</td>
		</tr>
		<tr >
			<td >Oligo aCGH/ChIP-on-chip Wash Buffer 2</td>
			<td >Agilent</td>
			<td >p/n 5188-5222</td>
			<td>Array CGH hybridization and wash</td>
		</tr>
		<tr >
			<td >Stabilization and Drying Solution</td>
			<td >Agilent</td>
			<td >p/n 5185-5979</td>
			<td>Array CGH hybridization and wash</td>
		</tr>
		<tr >
			<td >Oligo aCGH/ChIP-on-chip Hybridization Kit</td>
			<td >Agilent</td>
			<td >p/n 5188-5220 (25) or p/n 5188-5380 (100)</td>
			<td>Array CGH hybridization and wash</td>
		</tr>
		<tr >
			<td >Human Cot-1 DNA</td>
			<td >Agilent</td>
			<td >p/n 5190-3393</td>
			<td>Array CGH hybridization and wash</td>
		</tr>
		<tr >
			<td >Agilent C scanner</td>
			<td >Agilent</td>
			<td ></td>
			<td>Scanner for array CGH slides</td>
		</tr>
		<tr >
			<td >SureSelect XT2 Reagent Kit</td>
			<td ></td>
			<td ></td>
			<td>Kit for target enrichment</td>
		</tr>
		<tr >
			<td >HiSeq platform (HSQ), 16 Samples</td>
			<td >Agilent</td>
			<td >p/n G9621A</td>
			<td></td>
		</tr>
		<tr >
			<td >HiSeq platform (HSQ), 96 Samples</td>
			<td >Agilent</td>
			<td >p/n G9621B</td>
			<td></td>
		</tr>
		<tr >
			<td >HiSeq platform (HSQ), 480 Samples</td>
			<td >Agilent</td>
			<td >p/n G9621C</td>
			<td></td>
		</tr>
		<tr >
			<td >MiSeq platform (MSQ), 16 Samples</td>
			<td >Agilent</td>
			<td >p/n G9622A</td>
			<td></td>
		</tr>
		<tr >
			<td >MiSeq platform (MSQ), 96 Samples</td>
			<td >Agilent</td>
			<td >p/n G9622B</td>
			<td></td>
		</tr>
		<tr >
			<td >MiSeq platform (MSQ), 480 Samples</td>
			<td >Agilent</td>
			<td >p/n G9622C</td>
			<td></td>
		</tr>
		<tr >
			<td >DNA 1000 Kit</td>
			<td >Agilent</td>
			<td >p/n 5067-1504</td>
			<td>Kit for the separation, sizing and quantification of dsDNA fragments from 25 to 1000 bp.</td>
		</tr>
		<tr >
			<td >High Sensitivity DNA Kit</td>
			<td >Agilent</td>
			<td >p/n 5067-4626</td>
			<td>Kit for analysis of fragmented DNA or DNA libraries.</td>
		</tr>
		<tr >
			<td >AMPure XP Kit</td>
			<td ></td>
			<td ></td>
			<td>Kit for automated PCR purification.</td>
		</tr>
		<tr >
			<td >5 mL</td>
			<td >Agencourt</td>
			<td >p/n A63880</td>
			<td></td>
		</tr>
		<tr >
			<td >60 mL</td>
			<td >Agencourt</td>
			<td >p/n A63881</td>
			<td></td>
		</tr>
		<tr >
			<td >450 mL</td>
			<td >Agencourt</td>
			<td >p/n A63882</td>
			<td></td>
		</tr>
		<tr >
			<td >Dynabeads MyOne Streptavidin T1</td>
			<td ></td>
			<td ></td>
			<td>Isolation and handling of biotinylated nucleic acids</td>
		</tr>
		<tr >
			<td >2 mL</td>
			<td >Life Technologies</td>
			<td >Cat #65601</td>
			<td></td>
		</tr>
		<tr >
			<td >10 mL</td>
			<td >Life Technologies</td>
			<td >Cat #65602</td>
			<td></td>
		</tr>
		<tr >
			<td >Quant-iT dsDNA BR Assay Kit, for the Qubit fluorometer</td>
			<td ></td>
			<td ></td>
			<td>DNA quantification</td>
		</tr>
		<tr >
			<td >100 assays, 2-1000 ng</td>
			<td >Life Technologies</td>
			<td >Cat #Q32850</td>
			<td></td>
		</tr>
		<tr >
			<td >500 assays, 2-1000 ng</td>
			<td >Life Technologies</td>
			<td >Cat #Q32853</td>
			<td></td>
		</tr>
		<tr >
			<td >Qubit assay tubes</td>
			<td >Life Technologies</td>
			<td >p/n Q32856</td>
			<td>DNA quantification</td>
		</tr>
		<tr >
			<td >SureSelec tXT2 Capture Libraries</td>
			<td >Agilent</td>
			<td >depending on the experiment</td>
			<td>Kit for libraries capture</td>
		</tr>
		<tr >
			<td >SureCycler 8800 Thermal Cycler</td>
			<td >Agilent</td>
			<td >p/n G8800A</td>
			<td>DNA amplification</td>
		</tr>
		<tr >
			<td >96 well plate module for SureCycler 8800 Thermal Cycler</td>
			<td >Agilent</td>
			<td >p/n G8810A</td>
			<td>DNA amplification</td>
		</tr>
		<tr >
			<td >SureCycler 8800-compatible 96-well plates</td>
			<td >Agilent</td>
			<td >p/n 410088</td>
			<td>DNA amplification</td>
		</tr>
		<tr >
			<td >Optical strip caps</td>
			<td >Agilent</td>
			<td >p/n 401425</td>
			<td>DNA amplification</td>
		</tr>
		<tr >
			<td >Tube cap strips, domed</td>
			<td >Agilent</td>
			<td >p/n 410096</td>
			<td>DNA amplification</td>
		</tr>
		<tr >
			<td >Compression mats</td>
			<td >Agilent</td>
			<td >p/n 410187</td>
			<td>DNA amplification</td>
		</tr>
		<tr >
			<td >2100 Bioanalyzer Laptop Bundle</td>
			<td >Agilent</td>
			<td >p/n G2943CA</td>
			<td>DNA amplification</td>
		</tr>
		<tr >
			<td >2100 Bioanalyzer Electrophoresis Set</td>
			<td >Agilent</td>
			<td >p/n G2947CA</td>
			<td>DNA amplification</td>
		</tr>
		<tr >
			<td >Covaris Sample Preparation System, E-series or S-series</td>
			<td >Covaris</td>
			<td ></td>
			<td>DNA shearing</td>
		</tr>
		<tr >
			<td >Covaris sample holders</td>
			<td ></td>
			<td >p/n 520078</td>
			<td>DNA shearing</td>
		</tr>
		<tr >
			<td >Nutator plate mixer</td>
			<td >BD Diagnostics</td>
			<td >p/n 421105 or equivalent</td>
			<td>Plate Mixer</td>
		</tr>
		<tr >
			<td >GaIIx</td>
			<td >Illumina</td>
			<td ></td>
			<td>next generation sequencing machine</td>
		</tr>
	</tbody>
</table>

a novel strategy combining array-cgh, whole-exome sequencing and in utero electroporation in rodents to identify causative genes for brain malformations

Birth defects that involve the cerebral cortex &#8212; also known as malformations of cortical development (MCD) &#8212; are important causes of intellectual disability and account for 20-40% of drug-resistant epilepsy in childhood. High-resolution brain imaging has facilitated in vivo identification of a large group of MCD phenotypes. Despite the advances in brain imaging, genomic analysis and generation of animal models, a straightforward workflow to systematically prioritize candidate genes and to test functional effects of putative mutations is missing. To overcome this problem, an experimental strategy enabling the identification of novel causative genes for MCD was developed and validated. This strategy is based on identifying candidate genomic regions or genes via array-CGH or whole-exome sequencing and characterizing the effects of their inactivation or of overexpression of specific mutations in developing rodent brains via in utero electroporation. This approach led to the identification of the C6orf70 gene, encoding for a putative vesicular protein, to the pathogenesis of periventricular nodular heterotopia, a MCD caused by defective neuronal migration.

The experimental strategy designed to identify novel MCD causative genes is recapitulated in Figure 1.
By performing array-CGH in a cohort of 155 patients with developmental brain abnormalities variably combining PNH (Figure 2A), corpus callosum dysgenesis, colpocephaly, cerebellar hypoplasia and polymicrogyria associated with epilepsy, ataxia and cognitive impairment, we identified a 1.2 Mb min...

Watch this Scientific Journal Video about A Novel Strategy Combining Array-CGH, Whole-exome Sequencing and In Utero Electroporation in Rodents to Identify Causative Genes for Brain Malformations at Jo

A Novel Strategy Combining Array-CGH, Whole-exome Sequencing and In Utero Electroporation in Rodents to Identify Causative Genes for Brain Malformations

Periventricular nodular heterotopia (PNH) is the most common form of malformation of cortical development (MCD) in adulthood but its genetic basis remains unknown in most sporadic cases. We have recently developed a strategy to identify novel candidate genes for MCDs and to directly confirm their causative role in vivo.

A Novel Strategy Combining Array-CGH, Whole-exome Sequencing and In Utero Electroporation in Rodents to Identify Causative Genes for Brain Malformations

Birth defects that involve the cerebral cortex &#8212; also known as malformations of cortical development (MCD) &#8212; are important causes of ...

Research

JoVE Journal

Neuroscience

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Behavioral endocrinological research in humans as well as in animals suggests that testosterone plays a key role in social interactions. Studies in ...

In utero Electroporation followed by Primary Neuronal Culture for Studying Gene Function in Subset of Cortical Neurons

In utero Electroporation followed by Primary Neuronal Culture for Studying Gene Function in Subset of Cortical Neurons

In vitro study of primary neuronal cultures allows for quantitative analyses of neurite outgrowth. In order to study how genetic alterations affect ...

Combining Transcranial Magnetic Stimulation and fMRI to Examine the Default Mode Network

The default mode network is a group of brain regions that are active when an individual is not focused on the outside world and the brain is at "wakeful ...

Efficient Gene Delivery into Multiple CNS Territories Using In Utero Electroporation

Efficient Gene Delivery into Multiple CNS Territories Using In Utero Electroporation

The ability to manipulate gene expression is the cornerstone of modern day experimental embryology, leading to the elucidation of multiple developmental ...

Mouse in Utero Electroporation: Controlled Spatiotemporal Gene Transfection

Mouse in Utero Electroporation: Controlled Spatiotemporal Gene Transfection

In order to understand the function of genes expressed in specific region of the developing brain, including signaling molecules and axon guidance ...

Visualization and Genetic Manipulation of Dendrites and Spines in the Mouse Cerebral Cortex and Hippocampus using In utero Electroporation

Visualization and Genetic Manipulation of Dendrites and Spines in the Mouse Cerebral Cortex and Hippocampus using In utero Electroporation

In utero electroporation (IUE) has become a powerful technique to study the development of different regions of the embryonic nervous system 1-5. To date ...

Generation of Topically Transgenic Rats by In utero Electroporation and In vivo Bioluminescence Screening

Generation of Topically Transgenic Rats by In utero Electroporation and In vivo Bioluminescence Screening

 In utero electroporation (IUE) is a technique which allows genetic modification of cells in the brain for investigating neuronal development. So far, the ...

Deep Brain Stimulation with Simultaneous fMRI in Rodents

In order to visualize the global and downstream neuronal responses to deep brain stimulation (DBS) at various targets, we have developed a protocol for ...

Combining Double Fluorescence In Situ Hybridization with Immunolabelling for Detection of the Expression of Three Genes in Mouse Brain Sections

Combining Double Fluorescence In Situ Hybridization with Immunolabelling for Detection of the Expression of Three Genes in Mouse Brain Sections

Detection of gene expression in different types of brain cells e.g., neurons, astrocytes, oligodendrocytes, oligodendrocyte precursors and microglia, can ...

In Utero Electroporation Approaches to Study the Excitability of Neuronal Subpopulations and Single-cell Connectivity

In Utero Electroporation Approaches to Study the Excitability of Neuronal Subpopulations and Single-cell Connectivity

The nervous system is composed of an enormous range of distinct neuronal types. These neuronal subpopulations are characterized by, among other features, ...