With the development of sequencing technology, the cost of whole-genome sequencing was significantly declined.Meanwhile, with the application of combined whole-genome sequencing with epigenetic analysis on methylation and histone acetylation, the comprehensive and systematic analysis of numerous samples became a reality and we are able to re-understand the genesis and development of cancer. New ideas are emerging in comparative genomics research methods, from comparison of genomes among different individuals to horizontal self-comparison of different tissues and vertical self-comparison of genomes recently.Individualized diagnosis and treatment of cancer has shown a bright future.
Genome, Human ; genetics ; Humans ; Neoplasms ; genetics ; therapy ; Precision Medicine ; Sequence Analysis, DNA ; methods

OBJECTIVETo develop a solid phase PCR method by covalent single point immobilization for recycle utilization of human genome.

METHODSPolymethacrylamide gel was selected as a solid PCR carrier based on DNA-hydrogel copolymer chemistry presented by Mirzabekov. (CH2)6NH2 amino-modified PCR product and randomly fractured formic acid-modified plasmid pGEM-T-HLA-G were used as templates. The specificity of the attachment chemistry was characterized by acrylamide gel electrophoresis, and the thermal stability of method was demonstrated by PCR. This method was applied for the recycle utilization of human genome. Sequencing was used to exclude the possibility of introduced mutations during modification and immobilization procedures.

RESULTSThe PCR detections of plasmid DNA and human genome DNA immobilized by polymethacrylamide gel was successful. The thermal stability of method was successfully demonstrated by performing PCR after 16 rounds of standard 36 PCR cycles. And the sequencing was found no mutation.

CONCLUSIONThe DNA immobilization method with polymethacrylamide gel as a solid phase carrier is stable and specific, which can be a possible approach for realizing recycle utilization of human genome for whole-genome sequencing and SNP detection.

Electrophoresis, Polyacrylamide Gel ; Genome, Human ; Humans ; Hydrogels ; Immobilized Nucleic Acids ; analysis ; Polymerase Chain Reaction ; methods

OBJECTIVETo track and analyze two false positive cases from non-invasive prenatal testing for potential fetal aneuploidy.

METHODSThe two cases, respectively reported to have XO (+++) and T18 (1/20) XO(+), were analyzed with conventional karyotyping, fluorescence in situ hybridization (FISH) and massively parallel genomic sequencing (MPS).

RESULTSThe first fetus, who was suspected for XO(+++), was verified to have super female syndrome (47,XXX/46,XX) due to confined placental mosaicism by karyotyping of amniotic fluid cells, FISH analysis of placenta and massively parallel sequencing (MPS) of fetal tissue. The second fetus, suspected to have trisomy 18 (1/20) XO(+), was verified to have Turner syndrome by karyotyping, FISH and MPS analyses of umbilical cord blood cells. And the karyotype was 45,X[48]/46, X, der(X) del(X) (p11.21) del(X) (q13.3)[62].

CONCLUSIONNon-invasive prenatal testing carries a risk for false positive diagnosis of fetal sex chromosome and trisomy 18. Combined cytogenetic and molecular techniques are required to ensure an accurate diagnosis.

Adult ; Aneuploidy ; Chromosome Aberrations ; Diagnostic Errors ; False Positive Reactions ; Female ; Fetal Diseases ; diagnosis ; genetics ; Humans ; Pregnancy ; Prenatal Diagnosis ; Young Adult

OBJECTIVETo explore the origin and mechanism of small supernumerary marker chromosomes (sSMC) in order to facilitate genetic counseling.

METHODSChromosome karyotypes of two fetuses and their immediate family members were analyzed by conventional G banding. High-throughput whole genome sequencing was used to determine the origin of sSMCs.

RESULTSFetus 1 was shown to have a karyotype of 47,XY,+mar but with normal FISH and B ultrasound findings. Its father also had a 47,XY,+mar karyotype with normal FISH results and clinical phenotype. High-throughput genome sequencing revealed that fetus 1 and its father were both 46,XY,dup(21)(q11.2;q21.1) with a 6.2 Mb duplication of the long arm of chromosome 21. The fetus was born with normal phenotype and developed well. Its grandmother also had a karyotype of 46,XX,t(15;21)(q13;p13) with normal FISH result and clinical phenotype. The karyotypes of its mother and grandfather were both normal. Analysis of fetus 2 showed a 47,XY,+mar karyotype with normal FISH results. High-throughput genome sequencing suggested a molecular karyotype of 46,XX. The fetus was born with normal phenotype and developed well. The karyotypes of its parents were both normal.

CONCLUSIONConsidering their variable origins, identification of sSMC should combine conventional G banding analyses with high-throughput whole genome sequencing for precise delineation of the chromosomes.

Adult ; Amniotic Fluid ; chemistry ; Chromosome Banding ; Chromosome Disorders ; diagnosis ; embryology ; genetics ; Cytogenetics ; Female ; Fetal Diseases ; diagnosis ; genetics ; Genetic Markers ; Humans ; In Situ Hybridization, Fluorescence ; Infant, Newborn ; Karyotyping ; Male ; Pregnancy ; Prenatal Diagnosis ; Young Adult

OBJECTIVETo analyze the deletion region for two fetal cases with large Yq deletions in order to provide genetic counseling and prenatal diagnosis.

METHODSFor both cases, amniotic fluid samples were cultured and analyzed with G banding and fluorescence in situ hybridization (FISH). Multiplex polymerase chain reaction was also carried out to amplify 15 sequence tagged sites (STS) of azoospermia factor (AZF) on the Y chromosome.

RESULTSFor both samples, the karyotypes were determined as 46,X,del(Y)(pter→q11:). No heterochromatin was found in C band. The karyotypes of their fathers were 46,XY, and heterochromatin was found in C band. STS analyses suggested that only sY82, sY84 and sY86 in AZFa were amplifiable while the other 12 STS were negative in amniotic fluid for the first case, which indicated deletions of AZFb, AZFd and AZFc. No AZF deletion was found in its father. For the second case, all 15 STS were amplifiable in the amniotic fluid, suggesting no AZF deletion. No AZF deletion was found in its father too.

CONCLUSIONConventional karyotyping combined with FISH and molecular genetics techniques can enable characterization of AZF microdeletions and facilitate genetic counseling and prenatal diagnosis.

Adult ; Azoospermia ; genetics ; Chromosome Deletion ; Chromosomes, Human, Y ; genetics ; Female ; Fetal Diseases ; diagnosis ; genetics ; Genetic Counseling ; Humans ; In Situ Hybridization, Fluorescence ; Karyotyping ; Male ; Pregnancy ; Prenatal Diagnosis