DNA-PET library construction, sequencing and mapping.

<p>(A) The genomic DNA was randomly sheared to different size range. (B) The very narrow region DNA fragments were obtained after size selection. (C) The purified DNA fragments were circularized, <i>EcoP15I</i> digested, sequencing adaptor ligated, and finally sequenced by SOLiD sequencer. (D) PET mapping span distribution of 1 kb (blue), 10 kb (red) and 20 kb (green) libraries. Based on the mapping pattern, PETs can be distinguished as concordant PETs and discordant PETs.</p

Detection of Chromosomal Breakpoints in Patients with Developmental Delay and Speech Disorders

<div><p>Delineating candidate genes at the chromosomal breakpoint regions in the apparently balanced chromosome rearrangements (ABCR) has been shown to be more effective with the emergence of next-generation sequencing (NGS) technologies. We employed a large-insert (7–11 kb) paired-end tag sequencing technology (DNA-PET) to systematically analyze genome of four patients harbouring cytogenetically defined ABCR with neurodevelopmental symptoms, including developmental delay (DD) and speech disorders. We characterized structural variants (SVs) specific to each individual, including those matching the chromosomal breakpoints. Refinement of these regions by Sanger sequencing resulted in the identification of five disrupted genes in three individuals: guanine nucleotide binding protein, q polypeptide <i>(GNAQ),</i> RNA-binding protein, fox-1 homolog <i>(RBFOX3),</i> unc-5 homolog D (<i>C.elegans) (UNC5D</i>), transmembrane protein 47 (<i>TMEM47</i>), and X-linked inhibitor of apoptosis (<i>XIAP</i>). Among them, <i>XIAP</i> is the causative gene for the immunodeficiency phenotype seen in the patient. The remaining genes displayed specific expression in the fetal brain and have known biologically relevant functions in brain development, suggesting putative candidate genes for neurodevelopmental phenotypes. This study demonstrates the application of NGS technologies in mapping individual gene disruptions in ABCR as a resource for deciphering candidate genes in human neurodevelopmental disorders (NDDs).</p></div

SV identification based on the mapping pattern of dPET clusters.

<p>The dark red and pink arrows represent the 5′ and 3′ anchor regions of the dPET cluster, respectively. Black, white and blue horizontal lines represent chromosome segments. The red track represents the coverage of cPETs. The dotted lines indicate the connections between the two dPET clusters. The sub-types of insertions are as follows: (1) Intra-chromosomal direct forward insertion. (2) Intra-chromosomal direct backward insertion. (3) Intra-chromosomal inverted forward insertion. (4) Intra-chromosomal inverted backward insertion. (5) Deletion plus intra-chromosomal direct forward insertion. (6) Deletion plus intra-chromosomal inverted forward insertion. (7) Inter-chromosomal direct insertion. (8) Inter chromosome inverted insertion.</p

Reconstruction of the <i>BCR-ABL1</i> amplicon of K562.

<p>(A) Concordant tag distributions representing copy number are shown for amplified genomic regions (top, green track). Genomic segments between predicted breakpoints are indicated by colored arrows and dPET clusters with cluster sizes greater than 35 of predicted somatic rearrangements are represented by horizontal lines flanked by dark red and pink arrows indicating 5′ and 3′ anchor regions (middle). Small to large dPET clusters are arranged from top to bottom. Cluster sizes are indicated. High dPET cluster size of the CML causing <i>BCR-ABL1</i> translocation suggests that the rearrangement occurred early and that it has subsequently been amplified. Fusion points I–III correspond to panels C–D. (B) Fluorescence <i>in situ</i> hybridization (FISH) of <i>BCR-ABL1</i> rearrangement (fusion point I with cluster size 692). Yellow spots represent fusion signals and illustrate the amplification of <i>BCR-ABL1</i>. (C) FISH analysis of metaphase chromosomes of three high copy fusion points: I) probes used in B show fusion signals on two marker chromosomes and on chromosome 2q and normal localization on both rearranged chromosomes 9 and normal chromosome 22; the fusion on chromosome 2 has not been identified by DNA-PET most likely due to low sequence complexity at the break point or complex rearrangements, II) probes spanning the fusion point II (cluster size 259) show fusion signals on the same marker chromosomes and normal localization on both normal and rearranged chromosomes 9 and 13, III) probes spanning fusion point III (cluster size 218) show fusion signals on the same marker chromosomes and normal localization on both normal chromosome 22 and rearranged chromosomes 9. (D) Contigs (indicated by boxes) which were covered by PET mapping were concatenated by fusion-point-guided-concatenation method. The length of a contig is represented by the length of the box. Because of the size difference between chromosomes 1, 3, 9, 13, and 22, the length of chromosome 22 is represented by the length of contig/10,000 while the lengths of chromosomes 1, 3, 9, and 13 are represented by the length of contig/100,000. Any value less than 0.1 is rounded to 0.1; any value larger than 6 is rounded to 6. The thickness of borders of each contig represents the coverage (copy number). Red dashed edges represent dPET edges, while black bold edges represent cPET edges. The thickness of dPET edges represents the size of the corresponding dPET cluster. cPET edges have uniform thickness. Arrow heads pointing towards a contig indicate connections with the lower coordinates, arrow heads pointing away from a contig indicate connections with the higher coordinates.</p

Statistics of PET sequencing.

1)<p>non-redundant.</p>2)<p>physical coverage.</p>3)<p>concordant PET.</p>4)<p>proportion of cPET to total NR PET.</p>5)<p>discordant PET.</p>6)<p>proportion of dPET to total NR PET.</p>7)<p>number of dPET involved in the dPET clusters with cluster count ≥3.</p

List of SVs obtained after filtration of four patients.

a<p>Discordantly mapped PETs (dPETs) which connect the same two genomic regions are clustered together.</p>b<p>dPET clusters which has passed quality filters to remove sequencing artefacts provided the list of predicted SVs.</p>c<p>Approximately 95% of SVs overlapped with SVs found in normal population (see Methods).</p

Patient CD5 with translocation t(9;17).

<p>A) The pedigree of patient CD5 is indicated. The translocation is transmitted to his two sons (CD21 and CD22). B) Translocation between chromosome 9 and 17 were validated by Sanger sequencing in three translocation carriers. The reference sequence is indicated, showing the fusion of two genes at the genomic level: the first five exons of <i>GNAQ</i> fused to exon 3–14 of <i>RBFOX3</i> and the first two exons of <i>RBFOX3</i> fused to exon 6–7 of <i>GNAQ.</i> C) mRNA expression of <i>GNAQ</i> and <i>RBFOX3</i> showed high expression in fetal brain, adult brain and cerebellum in human tissue panel.</p

Screening of CNVs in cases/controls from published and public datasets.

<p>The total number of cases in Cooper et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090852#pone.0090852-Cooper1" target="_blank">[28]</a> is 15,767 cases, and for DECIPHER is ∼17,000 cases <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090852#pone.0090852-Swaminathan1" target="_blank">[29]</a>. The total number of controls in Cooper et al. is 8329 controls and for 1000 Genome SV Release set is 185 controls <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090852#pone.0090852-Mills1" target="_blank">[22]</a>.</p

Patient CD10 with translocation t(6;8).

<p>A) The pedigree of patient CD10 is indicated. The familial translocation is inherited from asymptomatic carrier mother and shared with his affected sister (CD11). B) Sanger sequencing analysis refined the chromosomal breakpoint regions and revealed a loss of 11 bp on chromosome 6 and 8 bp on chromosome 8, with a microhomology of 3 bp between the paired breakpoints. C) <i>UNC5D</i> mRNA expression in human tissue panel showed high expression in the fetal brain, adult brain and cerebellum compared to other tissues. D) The translocation breakpoint is located at intron 1 of <i>UNC5D</i> indicated by the black arrow, encompasses 15 CNVs cases described in the DECIPHER.</p

Patient CD8 with a complex chromosomal inversion.

<p>A) Karyogram of normal chromosome X compared to der(X) in patient CD8. B) FISH validation of 10 SVs shown in Table S5 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090852#pone.0090852.s001" target="_blank">Supporting Information S1</a>) with the respective FISH probes: Hybridization of RP1-296G17-Biot (SV15) and RP1-315-Dig (SV16) were localized on the centromere of the patient’s metaphase. Probes for SV17 and SV21 on Xp21 (RP11-330K13-Biot) and Xq25 (W12-499N23-Dig), respectively resulted in a split signal between Xp21 and the centromeric region in the patient’s chromosome. Further FISH analysis was performed by using probe RP11-762M23-Biot on Xq11.1 (SV22) that was found to localize on the upper chromosomal arm. Probe RP11-655E22 on Xp11.2 was localized on the lower arm of derivative chromosome X. C) Reconstructed derivative chromosome X for patient CD8. Normal human chromosome X according to ISCN 2009 with the arrow orientation from <i>a</i> to <i>d</i> and the proposed mechanism of sequential double inversion in patient CD8. Based on our FISH analysis, an inversion occurred first between Xp21 and Xq25, changing the orientation of p and q arm with a shift of the centromere position towards the lower q-arm shown by inverted red arrow <i>b</i> and <i>c</i>. This was followed by the second inversion that occurred between Xq11.1 and Xq25, altering the orientation of the q-arm (inverted green arrow <i>c</i>). D) Expression of <i>TMEM47</i> in human tissue panel assessed by qRT-PCR. E) Expression analysis of four disrupted genes in patient CD8 assessed by qRT-PCR.</p