What is the difference between insertion and translocation

Shaffer Lisa G. Google Preview. Read More. Your current browser may not support copying via this button. Subscriber sign in You could not be signed in, please check and try again. Username Please enter your Username. Password Please enter your Password.

Forgot password? Don't have an account? Sign in via your Institution. You could not be signed in, please check and try again. Parts of all the long reads that support the breakpoint in chromosome 9 were mapped to an alpha satellite near the gap caused by the centromere. Due to the gap region of the reference genome hg19 , the position of the breakpoint was imprecise. However, these long reads provide strong evidence that the breakpoint in the centromere region is consistent with the karyotyping results.

All these observations show the ability of long reads for breakpoint detection in such low complexity genome regions. Similar to balanced translocations, inversions do not change the chromosome copy number, and they are difficult to detect using conventional short-read sequencing technology, although they have vital functional consequences in medical genetics Puig et al.

Here, we successfully detected an inversion occurring in carrier DM17A at chr,,,, and chr,,,, Figure S2. After verification by PCR and Sanger sequencing, the breakpoints were finally identified as chr,, and chr,,, respectively, consistent with the karyotyping results.

Our results demonstrated an example where long-read sequencing was capable of accurately resolving complex breakpoints for inversions. To further validate the exact translocation breakpoints and neighboring SNPs, PCR and Sanger sequencing were performed to extract the breakpoint sequences at the level of single bases.

Because the approximate breakpoints in samples DM17A and DM17A were located in highly repetitive regions and the breakpoint in sample DM17A was near a centromere, it was challenging to obtain a PCR product for these breakpoints, despite multiple attempts.

Nevertheless, it is worth noting that for sample DM17A, we successfully obtained the target PCR bands from the normal chromosome without translocations , but no band was found reflecting rearranged chromosomes Figure S5 , suggesting that a deletion or larger insertion near the breakpoints may have broken the binding sites of our primers.

The results above further suggest the power of long-read sequencing in detecting the precise locations of translocation breakpoints, whereas karyotype analysis can only provide crude results at the megabase level.

Therefore, long-read sequencing may be a more precise tool for detecting translocation breakpoints and may complement or validate karyotyping results in clinical-diagnostic settings.

Haplotype identification of chromosomes is of great importance to PGD, such that adjacent SNP information can be used to predict the presence or absence of balanced translocations in single-cell assays. Here, we performed haplotype analysis by using the breakpoints as precise markers.

Haplotypes can help distinguish between embryos with balanced translocations and structurally normal chromosomes through PGD analysis in cases where the spouse of a carrier has a normal karyotype. These results demonstrate that it is possible to determine haplotypes by low-coverage long-read sequencing. Figure 3 Long-read sequencing enabled haplotype detection around the translocation breakpoints in sample DM17A Using the breakpoints as anchoring markers, we obtained 2-megabase sequences on either side of the breakpoints.

Reads around breakpoints were shown in IGV bottom panel and regions in red box were enlarged top panel. Capital letters represent accurate sequencing information, whereas lowercase letters represent fuzzy base information.

Since our study focused on translocations that were already identified by karyotyping, we did not perform a more detailed analysis for CNVs. However, these results and simulations demonstrate that even with low-coverage data, long-read sequencing still can detect a large number of potential CNVs and may be used to validate candidate CNVs that are detected by other platforms such as SNP arrays.

Currently, karyotype analysis is the most widely used technology for clinically diagnosing chromosomal translocations Comas et al. However, karyotype analysis is a low-resolution method that cannot identify exact breakpoints, which are often required for a better understanding of how translocations impact genes and phenotypes. However, because it generates short read lengths, paired-end or mate-pair libraries with large DNA inserts usually larger than 2 kb are always used for SV detection, as larger DNA insert sizes have been shown to be more advantageous in terms of SV detection in complicated DNA sequences, such as repetitive regions or large genomic rearrangements.

Moreover, larger DNA insert size libraries also provide higher physical coverage with minimum sequencing efforts than smaller insert sizes Yao et al. Nanopore technology yields longer reads than NGS. In this study, reads longer than kb were detected in each library, and we could obtain not only the two ends of the template generated by NGS, but also the entire DNA sequence.

Thus, we believe that nanopore is a more powerful tool for translocation and other SV detection. In this study, we analyzed genomic variations in seven patients with long-term reproductive disorders.

All seven patients carried chromosomal translocations in their genomes, with six having reciprocal balanced translocations and one having an inversion. We successfully identified and sequenced every breakpoint in these seven carriers by long-read sequencing. All 14 breakpoints identified by long-read sequencing were consistent with their corresponding karyotype results. This finding provides strong evidence that long-read sequencing shows flexibility in sequence preferences, even if the breakpoints appear in highly repetitive and complex regions.

Furthermore, PCR analysis of samples DM17A and DM17A showed clear target bands for the wild-type copies at the breakpoint sites but failed to generate any band for one or both breakpoints in the homologous chromosomes carrying the translocations. Reciprocal chromosome translocations are often accompanied with some additional rearrangements, such as deletions and duplications, involving only a few base pairs or up to millions of bases.

The failure in breakpoint identification by PCR in samples DM17A and DM17A may be due to the existence of this kind of rearrangement, where a deletion leads to loss of PCR primer-binding site s or a large insertion makes the PCR product too long to be amplified. In conclusion, by taking advantage of long reads, low-coverage whole-genome sequencing could be a more efficient and powerful tool for analyzing chromosomal translocations than traditional methods such as FISH and NGS.

By comparing karyotyping and Sanger sequencing results, we confirmed that nanopore sequencing exhibits high resolution and accuracy. We believe that long-read sequencing may play a more important role in chromosomal-translocation analysis and breakpoint detection in the future, as well as offer valuable insights for assisting the genetic diagnosis of reproduction and preimplantation. The research, including human subjects, human data and material, has been performed in accordance with the Declaration of Helsinki.

DW and GL directed the discussion of the manuscript. All authors approved the final manuscript. The authors want to thank patients who participated in this study to evaluate novel genomic approaches for improving genetic diagnosis of balanced translocations and inversions. We also thank the genetic counselors and clinical geneticists who interviewed the patients and collected DNA samples. We also thank Dr. Kai Wang for his guidance on structural variations analysis.

Abel, H. Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet. Alfarawati, S. First births after preimplantation genetic diagnosis of structural chromosome abnormalities using comparative genomic hybridization and microarray analysis. Aplan, P. Causes of oncogenic chromosomal translocation. Trends Genet. Callinan, P. Alu retrotransposition-mediated deletion. Collins, R. Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome.

These changes are not inherited; they occur in somatic cells cells other than eggs or sperm during the formation or progression of a cancerous tumor.

Other chapters in Help Me Understand Genetics. Genetics Home Reference has merged with MedlinePlus. Learn more. The information on this site should not be used as a substitute for professional medical care or advice. Contact a health care provider if you have questions about your health. Can changes in the structure of chromosomes affect health and development? From Genetics Home Reference. Changes in chromosome structure include the following: Translocations A translocation occurs when a piece of one chromosome breaks off and attaches to another chromosome.

Deletions Deletions occur when a chromosome breaks and some genetic material is lost. Duplications Duplications occur when part of a chromosome is abnormally copied duplicated. Inversions An inversion occurs when a chromosome breaks in two places; the resulting piece of DNA is reversed and re-inserted into the chromosome. Isochromosomes An isochromosome is a chromosome with two identical arms. A duplication happens when part of a chromosome is copied and additional genetic material is present.

When a chromosome has broken, rotated and reattached, an inversion has occurred. A pericentric inversion occurs in the centromere, and a paracentric inversion occurs in the p or q arms. Isochromosomes are another type structural abnormality in which the chromosome has two identical arms eg, two p arms.

A dicentric chromosome is a chromosome with two centromeres, and a ring chromosome is one in which the chromosome breaks in two places and the ends fuse together to form a ring shape. A gene mutation is a permanent change in the DNA sequence of a gene. Mutations can occur in a single base pair or in a large segment of a chromosome and even span multiple genes.

Mutations can result from endogenous occurring during DNA replication or exogenous environmental factors. There are two main categories of mutations: germline and somatic. A person with a germline mutation will have the mutation in every cell in the body. Germline mutations are the cause of some diseases, such as cystic fibrosis and cancer eg, breast and ovarian cancer, melanoma.

Cystic fibrosis is a hereditary genetic disorder that results in a thick, sticky buildup of mucus in the lungs, pancreas and other organs. Cystic fibrosis is the most common genetic disease and arises from a mutation in a single gene named the cystic fibrosis transmembrane regulator gene CFTR.

The location of this gene is on the long arm q of chromosome 7 position Some forms of breast cancer can be hereditary. On chromosome 9, the gene CDK2N instructs protein development. Proteins made by CDK2N include p16 and p