Comparison among the subjects’ genotypes and symptoms among samples.

<p>+: duplication, −: deletion, n: normal. Losing or gain in the whole segments leads to diseases. REPD variations may not leads to diseases but impacts SOX7 which is related to CHD.</p

CNs of genes in the family, other patients and normal controls.

<p>Left: Genes we detected. Right: CNs of the family, two patients, and other samples(50 controls and 48 patients); n: normal ratio comparing with the DNA pool. \: no data.</p

The copy number analysis of chromosome 8.

<p>(A) Ideogram of chromosome 8. (B) Results of SNP-array integrated with CNV probes. Blue spots, B allele freq; Red line, smoothed Log R; Genes were annotated: Red, deletion; Black, normal; Green, duplication. Regions of REPD and REPP were annotated in brown bar.</p

Primers for sequencing TBX-1, TBX-5, GATA-4, GATA-6, SOX7, Nkx2.5 and Fog2.

<p>Primers for sequencing TBX-1, TBX-5, GATA-4, GATA-6, SOX7, Nkx2.5 and Fog2.</p

The echocardiography images of this case.

<p>MPA: main pulmonary artery, RV: right ventricular, VSD: ventricular septal defect, IVS: inter ventricular septum, LV: left ventricular, AO: aortic artery.</p

Primers of the genes in qPCR.

<p>Primers of the genes in qPCR.</p

Additional file 1: of Rare copy number variants analysis identifies novel candidate genes in heterotaxy syndrome patients with congenital heart defects

Table S1. MO sequences, injection doses, and total embryo numbers analyzed for heart looping and gene expression. Table S2. Specific primers and vector used to produce genes’ full-length mRNA. Table S3. Antisense RNA probes conducted for whole mount in situ hybridization. Table S4. The frequency of each candidate CNV in normal Chinese individuals and non-heterotaxy patients with developmental delay/intellectual disability. Table S5. The function of the genes associated with the 19 rare CNV segments. Table S6. The bioinformatics information on the variant of LEFTY1 in the patient with CNV of TTC40 (CFAP46). Table S7. The bioinformatics information on the variants of candidate genes. (PDF 369 kb

Data_Sheet_1_Novel compound heterozygous CCDC40 mutations in a familial case of primary ciliary dyskinesia.ZIP

Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by motile ciliary dysfunction and impaired ultrastructure. Despite numerous studies, the genetic basis for about 30% of PCD cases remains to be elucidated. Here, we present the identification and functional analysis of two novel mutations in the gene encoding coiled-coil domain-containing protein 40 (CCDC40), which are found in a familial case of PCD. These novel CCDC40 mutations, NM_017950.4: c.2236-2delA and c.2042_2046delTCACA, NP_060420.2: p.(Ile681fs), were identified by whole-exome sequencing (WES). Sanger sequencing was then performed to confirm the WES results and determine the CCDC40 gene sequences of the proband’s parents. The c.2042_2046delTCACA mutation disrupts the reading frame of the protein and is therefore predicted to produce a non-functional protein. Using a minigene assay with the pcDNA3.1(+) plasmid, we further investigated the potential pathogenic effects of the c.2236-2delA mutation and found that this mutation leads to formation of a truncated protein via splicing disruption. Thus, in summary, we identified two mutations of the CCDC40 gene that can be considered pathogenic compound heterozygous mutations in a case of familial PCD, thereby expanding the known mutational spectrum of the CCDC40 gene in this disease.</p

Additional file 2: of Rare copy number variants analysis identifies novel candidate genes in heterotaxy syndrome patients with congenital heart defects

Figure S1. Knockdown efficiency of splice blocking and translation blocking MOs in zebrafish embryos. Figure S2. The knockout efficiency of dnah10 and rnf115 by CRISPR/Cas9. Figure S3. Chromosomal view of rare CNVs in candidate Htx patients and the verified results of qPCR. Figure S4. Gene sequencing peak shows a nonsynonymous heterozygous mutation in LEFTY1 in the patient with CNV of TTC40 (CFAP46). Figure S5. Rare variations were detected in Htx patients. (PDF 792 kb

MOESM1 of A loss-of-function mutation p.T52S in RIPPLY3 is a potential predisposing genetic risk factor for Chinese Han conotruncal heart defect patients without the 22q11.2 deletion/duplication

Additional file 1: Table S1. Primer pairs used to amplify the coding regions contain candidate variants. Table S2. Primer pairs used to amplify the TBX1C variants identified in patients harboring RIPPLY3 variants. Figure S1. Subcellular localization of wild-type TBX1 protein in transiently transfected HEK293T cells. The wild-type TBX1 localized exclusively to the nuclei with normal nuclear distribution