Metastatic pattern and prognosis of gastrointestinal stromal tumor (GIST): a SEER-based analysis.

PURPOSE: This SEER-based study aimed to explore and analyze the relationship of metastasis of liver, lung and bone of GIST patients and their prognosis. METHODS: The data of GIST patients were from Surveillance, Epidemiology, and End Results (SEER) database from 2010 to 2015 and all the statistical analyses were conducted by statistical software package SPSS (Version 22.0). RESULTS: A total of 4224 GIST patients were identified, of which 388 (9.19%) patients with liver metastasis, 20 (0.47%) patients with bone metastasis and 32 (0.76%) patients with lung metastasis. There was no significant difference of risk of bone or lung metastasis between patients with and without liver metastasis (P = 0.935). The median overall survival of patients with liver, bone, or lung metastasis was, respectively, 49 months, 18 months, and 20 months, which were all shorter than that of patients without metastasis. The overall survival of patients with both liver and bone metastasis and those with metastasis of all three sites was not significantly different from that of patients with only liver metastasis. The multivariate analysis showed age of less than 65 years, female patients, married status and receiving surgery were all the beneficial factors for prognosis of GIST patients with liver metastasis. CONCLUSIONS: Patients with metastasis had a poorer prognosis than those without. Liver metastasis might have no relationship with bone or lung metastasis and liver might play a more dominant role than the other two sites in the prognosis of GIST patients with metastasis. So, more attention should be paid to liver status in diagnosis and treatment of GIST patients.

Isolation and characterization of microsatellite markers for Dendranthema morifolium (Asteraceae) using next-generation sequencing.

Dendranthema morifolium (Asteraceae) is a perennial herbaceous plant native to China. A long history of artificial crossings may have resulted in complex genetic background and decreased genetic diversity. To protect the genetic diversity of D. morifolium and enabling breeding of new D. morifolium cultivars, we developed a set of molecular markers. We used pyrosequencing of an enriched microsatellite library by Roche 454 FLX+ platform, to isolate D. morifolium simple sequence repeats (SSRs). A total of 32,863 raw reads containing 2251 SSRs were obtained. To test the effectiveness of these SSR markers, we designed primers by randomly selecting 100 novel SSRs, and amplified them across 60 cultivars representing five different petal shape groups. Sixteen SSRs were polymorphic with the number of alleles ranging from 6 to 19, and their expected and observed heterozygosities ranging from 0.477 to 0.848, and 0.250 to 0.804, respectively. The polymorphism information content ranged from 0.459 to 0.854 and the inbreeding coefficient ranged from -0.119 to 0.759. An unweighted pair-group method arithmetic average analysis was performed to survey the phylogenetic relationships of these 60 cultivars and five clusters were identified. These markers can be used for investigating genetic relationships and identifying elite alleles through linkage and association analyses.

Isolation and characterization of microsatellite markers for Eucommia ulmoides (Eucommiaceae), an endangered tree, using next-generation sequencing.

Eucommia ulmoides Oliver, a single extant species of Eucommiaceae, is an endemic dioecious tree in China. The natural resources of E. ulmoides have rapidly declined in recent years because of the over-collection of its cortex. To design a suitable protection strategy, it is necessary to develop a set of molecular markers to investigate genetic diversity and population structure of E. ulmoides. Pyrosequencing of an enriched microsatellite library by Roche 454 FLX+ platform was used to isolate simple sequence repeats (SSRs) for E. ulmoides. A total of 1568 SSRs that contained enough flanking sequences for primer pair design were identified from 45,236 raw sequence reads. One hundred SSRs were randomly selected to design primer pairs and polymerase chain reaction was performed. Among these 100 tested primer pairs, 16 were polymorphic across 18 individuals from three E. ulmoides populations. The number of alleles ranged from 3 to 8, with an average of 5.1. The expected heterozygosity ranged from 0.110 to 0.830, with an average of 0.648, and the observed heterozygosity ranged from 0.111 to 0.833, with an average of 0.524. The inbreeding coefficient ranged from -0.349 to 0.547. This set of microsatellite markers could be valuable for landscape genetic structure assessment and molecular marker-assisted breeding in E. ulmoides.

Isolation and characterization of microsatellite markers for Osmanthus fragrans (Oleaceae) using 454 sequencing technology.

Osmanthus fragrans (Oleaceae) is an evergreen shrub or small tree that grows in south China. In this study, Roche 454 FLX+ sequencing combined with the magnetic bead enrichment method was used to isolate microsatellite markers from the genome of O. fragrans. A total of 1471 microsatellites that contained enough flanking sequences for primer pair design were identified from 89,633 raw sequencing reads. One hundred primer pairs were randomly chosen to test primer amplification efficiency. Among these tested primer pairs, 20 yielded polymorphic amplification products across 16 individuals from the Albus, Luteus, and Aurantiacus groups. The number of alleles ranged from 2 to 6, with an average of 3.7. The observed heterozygosity ranged from 0 to 0.813, with an average of 0.460. Shannon's information index ranged from 0.463 to 1.707, with an average of 0.975. Six loci (Of 05, Of 06, Of 08, Of 12, Of 15, and Of 19) deviated significantly from Hardy-Weinberg equilibrium (P < 0.05), which was due to an excess of homozygotes or heterozygotes. Nine pairs of loci (Of 01 and Of 05; Of 04 and Of 05; Of 01 and Of 06; Of 04 and Of 12; Of 02 and Of 13; Of 04 and Of 13; Of 12 and Of 13; Of 04 and Of 19; Of 05 and Of 19) showed significant linkage disequilibrium, which indicated significant allelic association between the loci. This set of microsatellite markers will be valuable for molecular marker-assisted breeding in O. fragrans.