Breakpoints and deleted genes identification of ring chromosome 18 in a Chinese girl by whole-genome low-coverage sequencing: a case report study

The serological examination results. (DOCX 13 kb

Nitrate reductase is required for sclerotial development and virulence of Sclerotinia sclerotiorum

Sclerotinia sclerotiorum, the causal agent of Sclerotinia stem rot (SSR) on more than 450 plant species, is a notorious fungal pathogen. Nitrate reductase (NR) is required for nitrate assimilation that mediates the reduction of nitrate to nitrite and is the major enzymatic source for NO production in fungi. To explore the possible effects of nitrate reductase SsNR on the development, stress response, and virulence of S. sclerotiorum, RNA interference (RNAi) of SsNR was performed. The results showed that SsNR-silenced mutants showed abnormity in mycelia growth, sclerotia formation, infection cushion formation, reduced virulence on rapeseed and soybean with decreased oxalic acid production. Furthermore SsNR-silenced mutants are more sensitive to abiotic stresses such as Congo Red, SDS, H2O2, and NaCl. Importantly, the expression levels of pathogenicity-related genes SsGgt1, SsSac1, and SsSmk3 are down-regulated in SsNR-silenced mutants, while SsCyp is up-regulated. In summary, phenotypic changes in the gene silenced mutants indicate that SsNR plays important roles in the mycelia growth, sclerotia development, stress response and fungal virulence of S. sclerotiorum

Maternal interchromosomal insertional translocation leading to 1q43-q44 deletion and duplication in two siblings

Abstract Background 1q43-q44 deletion syndrome is a well-defined chromosomal disorder which is characterized by moderate to severe mental retardation, and variable but characteristic facial features determined by the size of the segment and the number of genes involved. However, patients with 1q43-q44 duplication with a clinical phenotype comparable to that of 1q43-q44 deletion are rarely reported. Moreover, pure 1q43-q44 deletions and duplications derived from balanced insertional translocation within the same family with precisely identified breakpoints have not been reported. Case presentation The proband is a 6-year-old girl with profound developmental delay, mental retardation, microcephaly, epilepsy, agenesis of the corpus callosum and hearing impairment. Her younger brother is a 3-month-old boy with macrocephaly and mild developmental delay in gross motor functions. G-banding analysis of the subjects at the 400-band level did not reveal any subtle structural changes in their karyotypes. However, single-nucleotide polymorphism (SNP) array analysis showed a deletion and a duplication of approximately 6.0 Mb at 1q43-q44 in the proband and her younger brother, respectively. The Levicare analysis pipeline of whole-genome sequencing (WGS) further demonstrated that a segment of 1q43-q44 was inserted at 14q23.1 in the unaffected mother, which indicated that the mother was a carrier of a 46,XX,ins(14;1)(q23.1;q43q44) insertional translocation. Moreover, Sanger sequencing was used to assist the mapping of the breakpoints and the final validation of those breakpoints. The breakpoint on chromosome 1 disrupted the EFCAB2 gene in the first intron, and the breakpoint on chromosome 14 disrupted the PRKCH gene within the 12th intron. In addition, fluorescence in situ hybridization (FISH) further confirmed that the unaffected older sister of the proband carried the same karyotype as the mother. Conclusion Here, we describe a rare family exhibiting pure 1q43-q44 deletion and duplication in two siblings caused by a maternal balanced insertional translocation. Our study demonstrates that WGS with a carefully designed analysis pipeline is a powerful tool for identifying cryptic genomic balanced translocations and mapping the breakpoints at the nucleotide level and could be an effective method for explaining the relationship between karyotype and phenotype

Mapping Breakpoints of Complex Chromosome Rearrangements Involving a Partial Trisomy 15q23.1-q26.2 Revealed by Next Generation Sequencing and Conventional Techniques.

Complex chromosome rearrangements (CCRs), which are rather rare in the whole population, may be associated with aberrant phenotypes. Next-generation sequencing (NGS) and conventional techniques, could be used to reveal specific CCRs for better genetic counseling. We report the CCRs of a girl and her mother, which were identified using a combination of NGS and conventional techniques including G-banding, fluorescence in situ hybridization (FISH) and PCR. The girl demonstrated CCRs involving chromosomes 3 and 8, while the CCRs of her mother involved chromosomes 3, 5, 8, 11 and 15. HumanCytoSNP-12 Chip analysis identified a 35.4 Mb duplication on chromosome 15q21.3-q26.2 in the proband and a 1.6 Mb microdeletion at chromosome 15q21.3 in her mother. The proband inherited the rearranged chromosomes 3 and 8 from her mother, and the duplicated region on chromosome 15 of the proband was inherited from the mother. Approximately one hundred genes were identified in the 15q21.3-q26.2 duplicated region of the proband. In particular, TPM1, SMAD6, SMAD3, and HCN4 may be associated with her heart defects, and HEXA, KIF7, and IDH2 are responsible for her developmental and mental retardation. In addition, we suggest that a microdeletion on the 15q21.3 region of the mother, which involved TCF2, TCF12, ADMA10 and AQP9, might be associated with mental retardation. We delineate the precise structures of the derivative chromosomes, chromosome duplication origin and possible molecular mechanisms for aberrant phenotypes by combining NGS data with conventional techniques

Additional file 2: of Maternal interchromosomal insertional translocation leading to 1q43-q44 deletion and duplication in two siblings

Table S2. The list of primers for PCR amplification of chromosomal breakpoint regions. (DOCX 16 kb

Additional file 1: of Maternal interchromosomal insertional translocation leading to 1q43-q44 deletion and duplication in two siblings

Table S1. The Gesell Development Scale results of the patients. (DOCX 16 kb

Analysis of genes involved in the variation region on different chromosome.

<p>Analysis of genes involved in the variation region on different chromosome.</p

Representative images from FISH analysis of the proband’s mother.

<p>(A) FISH using the Telomere 3p probe (spectrum green) and the Telomere 3q probe (spectrum red) revealed a green and red signal on der(3), indicating that the bottom of der(3) was the region of the translocation chromosome. (B) FISH using the Telomere 5p probe (spectrum green) and the Telomere 5q probe (spectrum red) revealed the absence of the red signal and presence of the green signal on der(5), as well as the presence of the red signal on der(11), indicating that telomere 5q was translocated to chromosome 11. (C) FISH using the Telomere 8p probe (spectrum green) and the Telomere 8q probe (spectrum red) revealed the absence of the red signal and presence of the green signal on der(8), as well as the presence of the red signal on der(3), indicating a translocation of 8q to chromosome 3. (D) FISH using the Telomere 15q probe (spectrum red) showed the presence of the red signal on der(15), indicating subtelomeric 15q sequences were retained on der(15) with a subterminal deletion on der(15). (E) FISH using probe D5S23 (spectrum green) at 5p15 and the probe EGR1 (spectrum red) at 5q31 revealed the absence of the red signal and presence of the green signal on distal der(5)’ short arm, as well as the presence of the red signal on der(11), indicating an inversion on the distal short arm of der(5)’. (F) FISH using the probe ETO (spectrum green) at 8q22 and the probe AML1 (spectrum red) at 21q22 showed the presence of the red signal on der(8) and the presence of the green signal on 21, indicating a breakpoint on chromosomes 8q22; the 22q regions of 21 were normal.(G)The MLL probe SCN4B (spectrum green) and TREH (spectrum red) at 11q23 showed the presence of the green and red signal on der(5), indicating a reciprocal translocation between chromosomes 11q and 5q. (H) FISH using probe D15Z1 (spectrum aqua) at 15p11.2, SNRPN (spectrum red) at 15q12 and PML (spectrum green) at 15q24.1 showed the presence of the aqua and red signal on der(15), as well as the presence of the green signal on der(3), indicating a reciprocal translocation between chromosomes 15q and 3q. (I) Probes used with FISH for the detection of chromosome breakpoints as well as CCRs. Reversed arrow demonstrates an inversion region.</p

Chromosome G-banding karyotype showing a complex chromosome rearrangement of the proband and her mother.

<p>(A) Aberrant chromosomes 3 and 5 of the proband. (B) CCRs between chromosomes 3, 5, 8, 11 and 15 of the mother. (C). Normal karyotype of the father. Arrows point to derivative chromosomes.</p

Sequencing results of the CCRs of the mother.

<p>Partial karyotype and ideogram of the proband’s mother showed the exceptional CCRs between chromosomes 3, 5, 8, 11 and 15. Reversed arrow indicates chromosome inversion.</p