Thursday, May 23, 2019

Readying the release of GRCm39


GRCm38, the current mouse reference assembly, whose chromosomes represent the C57BL/6J strain, supports a broad range of research activities. Despite being one of the highest quality mammalian genome assemblies ever produced, it still has more than 600 gaps and includes sub-optimal representations for some genes. To address these issues and provide the murine research community with an improved substrate for their work, the GRC has been applying new technologies, such as optical/genome mapping, and using new sequence resources to curate an update to the reference genome assembly. The public release of the updated assembly, GRCm39, is planned for the end of 2019/early 2020.

Since the 2012 release of GRCm38, the last coordinate-changing update to the mouse reference, the GRC has provided 6 publicly accessible minor assembly updates, the last of which (GRCm38.p6) was released in September, 2017. These non-coordinate changing assembly versions, known as patch releases, cumulatively include 65 fix patches (chromosome path changes) and 9 novel patches (alternate representations of chromosome sequences, derived from other strains). In GRCm39, these fix patches will be incorporated into the chromosomes, and the novel patches will persist as alternate loci.

In preparation for the release of GRCm39, the GRC also analyzed a non-public updated version of the reference assembly. In the production of this updated assembly, 322 reported genome issues were resolved, 70% of which addressed gaps and problems with the sequence of underlying genomic clone components. The review evaluated the value and impact of the released patches and subsequent unreleased genome updates and assessed the need for additional work prior to the GRCm39 release.

Analyses of this assembly, known informally as "GRCm38B", reveal the removal of about 200 Kb over-expanded sequence found in GRCm38, and the addition of 254 new components, of which 95 are contigs assembled from WGS reads (PRJNA51977). Due to the curation effort, GRCm38B has fewer gaps, and increased contig and scaffold N50s in comparison to GRCm38 (Table 1).


Furthermore, an analysis of mouse RefSeq transcripts aligned to GRCm38B demonstrates the improved representation for at least 50 genes (Table 2).


One such example of improved gene representation in GRCm38B is shown in Figure 1. In GRCm38, an assembly gap at chromosome 4 nt 99,842,111, between components BX324127.8 and CU326395.5, results in a partial representation of Efcab7 (EF-hand calcium binding domain 7). In GRCm38B, sequences from MF597759.1 (a GRC-assembled contig of Illumina reads) closes this gap and provides the exons missing from Efcab7 transcript NM_145549.1.
Figure 1 Top: Incomplete representation of Efcab7 gene in GRCm38 due to an assembly gap. Middle: The gap is closed in GRCm38B with MF597759.1. It also provides complete representation of Efcab7. Bottom: Efcab7-mRNA partial representation in GRCm38 and complete representation in GRCm38B.

Based on GRCm38B analyses, 5 GRCm39 chromosomes will be comprised of a single scaffold (Chr. 11, 12, 15, 16, 18), 11 will be built from 2 scaffolds and the remaining 5 from more than 2 scaffolds.

In the months leading up to the GRCm39 release, the GRC will continue to curate additional genome issues. Sequences from the recently published C57BL/6J long-read based assembly ASM377452v2 are providing new resources for the update or closure of assembly gaps and correction of sequencing errors. Additionally, we are investigating individual bases at which the GRCm38 sequence differs from all 17 strain-specific genome assemblies (Mouse Genome Project) with the aim of correcting confirmed erroneous bases.

Upon the release of GRCm39, the GRC's curation of the mouse genome reference assembly will be limited to the resolution of community reported problems.

You can browse the status of GRC curation activities at our website, and we encourage you to contact the GRC for additional information on the curation of assembly regions of interest. Updates to the timeline for the GRCm39 release will be provided on the Mouse Genome Overview webpage. You can also subscribe to grc-announce email list to receive email notification for all GRC assembly updates .

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  39. I'm 40 years old female I tested genital herpes (HSV1-2) positive in 2002. I was having bad outbreaks. EXTREMELY PAINFUL. I have try different kinds of drugs and treatment by the medical doctors all to know was avail. Six months ago I was desperately online searching for a helpful remedies for genital herpes (HSV1-2) cure, which i come across some helpful remedies on how Dr OYAGU have help so many people in curing genital herpes (HSV1-2) with the help of herbal treatment because I too believe there is someone somewhere in the world who can cure herpes completely. At of the past 2 months, however, I've been following his herpes protocol Via oyaguherbalhome@gmail.com or +2348101755322 and it stopped all outbreaks completely! To my greatest surprise I was cured completely by following the protocol of his herbal medicine . Don't be discouraged by the medical doctors. There is a cure for HSV with the help of herbs and roots by a herbalist Dr call Dr OYAGU he is so kind and truthful with his herbal treatment, kindly contact him for more information Via oyaguherbalhome@gmail.com or WhatsApp DR on +2348101755322 or vist his website https://oyaguspellcaster.wixsite.com/oyaguherbalhome you will be lucky as i am today

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  42. God bless Dr. USELU for his marvelous work in my life, I was diagnosed of HERPES SIMPLEX VIRUS since 2018 and I was taking my medications, I wasn’t satisfied i needed to get the HERPES out of my system, I searched about some possible cure for HERPES i saw a comment about Dr. USELU , how he cured HERPES with his herbal medicine, I contacted him and he guided me. I asked for solutions, he started the remedy for my health, he sent me the medicine within 3 days. I took the medicine as prescribed by him and 2weeks later i was cured from HERPES contact him via email (dr.uselucaregiver@gmail.com) once again thanks to you Dr. USELU cure the flowing virus, contact his email or add him on whatsapp (+2347052898482) cancer cure
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  43. I'm 40 years old female I tested genital herpes (HSV1-2) positive in 2002. I was having bad outbreaks. EXTREMELY PAINFUL. I have try different kinds of drugs and treatment by the medical doctors all to know was avail. Six months ago I was desperately online searching for a helpful remedies for genital herpes (HSV1-2) cure, which i come across some helpful remedies on how Dr OYAGU have help so many people in curing genital herpes (HSV1-2) with the help of herbal treatment because I too believe there is someone somewhere in the world who can cure herpes completely. At of the past 2 months, however, I've been following his herpes protocol Via oyaguherbalhome@gmail.com or +2348101755322 and it stopped all outbreaks completely! To my greatest surprise I was cured completely by following the protocol of his herbal medicine . Don't be discouraged by the medical doctors. There is a cure for HSV with the help of herbs and roots by a herbalist Dr call Dr OYAGU he is so kind and truthful with his herbal treatment, kindly contact him for more information Via oyaguherbalhome@gmail.com or WhatsApp DR on +2348101755322 or vist his website https://oyaguspellcaster.wixsite.com/oyaguherbalhome you will be lucky as i am today

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  44. Greetings to Everyone one on this Platform Who is taking their time to Read and to The Creative mind behind this incredible Platform. I want to use this medium to let everyone know that Herpes Simplex Virus has a complete and Permanent cure and that Dr Razor Herbal Medicine is the solution. I was Diagnosed with Herpes Virus type 1 in January 16, 2015, I have made several Research Hoping to see a true Cure or Healer, Fortunately for me i saw on a blog site how Dr Razor has been saving different lives and marriages with his herbal medicine, At first i did not believe but on a second thought, i decided to give him a try, I contacted him and he assured me of a cure, he prepared the herbal medication for me, which i took for 18 days, he told me to go for a medical check up, could you believe that i was confirm Herpes type 1 Negative after the test, and i went to a different hospital and it was also Negative, I became very happy and decided to write my appreciation article about this Good man. If you are battling with this same Infection or you know of a person who is infected with any disease like Herpes, HIV, Cancer, Syphilis, Hepatitis A,B,C, all types of Cancer, Gonorrhea, life's problems that you might have etc. kindly Reach out to Doctor Razor on Email : drrazorherbalhome@gmail.com. Whatsapp/Call him on +2349065420442. Visit Doctor Razor's website : https://herbalistrazorherb.wixsite.com/drrazorherbalhome .  My Sincere Gratitude to you Sir, God will surely Keep you safe from harm's way. Please share so Other lives can be saved

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  45. God bless Dr. USELU for his marvelous work in my life, I was diagnosed of HERPES SIMPLEX VIRUS since 2018 and I was taking my medications, I wasn’t satisfied i needed to get the HERPES out of my system, I searched about some possible cure for HERPES i saw a comment about Dr. USELU , how he cured HERPES with his herbal medicine, I contacted him and he guided me. I asked for solutions, he started the remedy for my health, he sent me the medicine within 3 days. I took the medicine as prescribed by him and 2weeks later i was cured from HERPES contact him via email (dr.uselucaregiver@gmail.com) once again thanks to you Dr. USELU cure the flowing virus, contact his email or add him on whatsapp (+2347052898482) cancer cure
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  46. DR OYAGU herbal medicine is a good remedy for herpes simplex virus cure. My name is MIGNON WRIGHT , am from USA,I am here to give my testimony about DR OYAGU who helped me in my life, i want to inform the public how i was cured from (HERPES SIMPLEX VIRUS) by DR OYAGU, i visited different hospital but they gave me list of drugs like Familiar, Zovirax, and Valtrex which is very expensive to treat the symptoms and never cured me. I was browsing through the Internet searching for remedy on HERPES and i saw comment of people talking about how DR OYAGU cured them, when i contacted him he gave me hope and send a Herbal medicine to me that i took and it seriously worked for me, am a free person now without any problem, my HERPES result came out negative, I pray to God to never let me and my family forget you in our life,am now cured permanently, you can also get your self cured my friends if you really need this doctor help, you can reach him now his website https://oyaguspellcaster.wixsite.com/oyaguherbalhome Email: oyaguherbalhome@gmail.com or via whatsapp +2348101755322

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  48. DR OYAGU herbal medicine is a good remedy for herpes simplex virus cure. My name is MIGNON WRIGHT , am from USA,I am here to give my testimony about DR OYAGU who helped me in my life, i want to inform the public how i was cured from (HERPES SIMPLEX VIRUS) by DR OYAGU, i visited different hospital but they gave me list of drugs like Familiar, Zovirax, and Valtrex which is very expensive to treat the symptoms and never cured me. I was browsing through the Internet searching for remedy on HERPES and i saw comment of people talking about how DR OYAGU cured them, when i contacted him he gave me hope and send a Herbal medicine to me that i took and it seriously worked for me, am a free person now without any problem, my HERPES result came out negative, I pray to God to never let me and my family forget you in our life,am now cured permanently, you can also get your self cured my friends if you really need this doctor help, you can reach him on his website https://oyaguspellcaster.wixsite.com/oyaguherbalhome Email: oyaguherbalhome@gmail.com or via whatsapp +2348101755322

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  49. Hello Am From The UK , I want to write a little testimony about the good work of doctor Oyagu who cured me from Hsv 1 and 2 for just 2 weeks with his herbal medicine, I never believe I can be normal again and have a good life like others I always regretted the day I got diagnose with the virus, I was lost of hope when my doctor told me there is no cure for it but I keep thinking and thinking about my future, if I can have kids of my own well I am so grateful for my helper who get me cured with his herbal medicine, I go online in search of anything that can help me because I can’t deal with it forever so I found this doc Oyagu email on a blog of someone who was cured by him I quickly contact him for help and explain all my pain to him, he told me not to worry about it there is cure for real, I never believe until he send me the herbal medicine when I order for it and I have it within 4 days that is how I took the medicine for 2 week and the following week I go for test just to confirm I was 100% cured from this sickness what a miracle in my life I am so happy right now, you can also get in contact with him if you have such sickness through email address oyaguherbalhome@gmail.com or text him on what's app, phone number +2348101755322 or vist his website https://oyaguspellcaster.wixsite.com/oyaguherbalhome Dr Oyagu also has remedy to others disease like COLD SORES,HIV/AIDS,DIABETES.CANCER,HIGH BLOOD PRESSURE AND MANY MORE. I oblige everyone to contact this powerful herbalist Dr Oyagu and be free from suffering.

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  50. I want to share my happiness to the world on how i was cured from (HERPES VIRUS) by Dr Oseremen herbal , i visited different hospital but they gave me list of drugs like Famvir, Zovirax, and Valtrex which is very expensive to treat the symptoms, but i did not have that kind of money to buy the drugs.the one i used before did not cured me. on one faithful day, a friend of my in united kingdom told me about Dr Oseremen herbal, he told me that,it is the herbal treatment that cure is husband from hepatitis B and she told me that he have cure so many people from herpes virus with is herb medicine,then she told me to contact him that he we cure me with is herb . when i contacted Dr Oseremen, he gave me hope and say that i we be cure once i get his herbal, he send the Herbal medicine to me and i take it for two weeks and it seriously worked for me, i went to the hospital to check, my HERPES result came out negative. I am so happy as i am sharing this testimony. My advice to you all who thinks that there is no cure for herpes that is Not true, just contact him and get cure from Dr Oseremen healing herbs, he also have the herb to cure any kind of hepatitis B,C A. AND DIFFERENT KIND OF SICKNESS Remember delay in treatment leads to death.. contact Dr Oseremen on is email at (Dr.Oseremenvadi@gmail.com) or whatsapp him on is Number :+2349056394313 and he we cure you with is HEALING HERB MEDICINE , thanks to Dr  Oseremen for cure me is healing herbs medicine

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  51. I already gave up on ever getting cured of HSV2 because i have try many treatment none of them work out for me i have be to different hospital they always tell me same thing there is no cure for herpes when i came across a post about Dr oyagu, in the net from a lady called Rebecca i contacted him and he reassured me with his herbal medicine which i took according to the way he instructed, that how i was cured. I doubted at first because i have been to a whole lot of reputable doctors, tried a lot of medicines but none was able to cure me. so i decided to listen to him and he commenced treatment, and under two weeks i was totally free from Herpes. i want to say a very big thank you to DR oyagu for what he has done in my life. feel free to leave him a message on email oyaguherbalhome@gmail.com and also WhatsApp him +2348101755322.. or vist his website https://oyaguspellcaster.wixsite.com/oyaguherbalhome. He can still be able to help you with this herbs medicine: 1...ALS CURE/DIABETES CURE/EPILESY/HPV CURE/LUPUS/HEPATITIS/CANCER/GOUT

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  53. DON'T BELIEVE THERE IS A CURE FOR HERPES? Well here is my testimony about a doctor who helped me when I was infected with HERPES on September 22, 2014, I went to many hospitals for cure but there was no solution, so I was thinking how can I get a solution so that my body can be okay. One day I was online and i saw the testimony of Mrs Amy Kendral speaking on how a man called Dr Razor helped her Eradicate the Herpes Simplex Infection that was eating her up every day, I Immediately emailed the Herbal Doctor Razor with the Details provided by This Woman on how to reach Him and I explained everything to him. Dr Razor told me all the things I needed to do and also gave me instructions to take a wish I followed properly. Before I knew what was happening after 18 days of taking the medication I started having changes in my body, so i told the herbalist of the development in my health and he asked me to go for a medical check up, the Doctors There were Amazed that Herpes have a Permanent and complete cured. Doctor Razor's website :  https://herbalistrazorherb.wixsite.com/drrazorherbalhome. You can Reach him on his Email via drrazorherbalhome@gmail.com . WhatsApp/Call him on +2349065420442. I made sure the Virus wasn't laying dormant in my nerve cells because I have heard of a situation like that. Before deciding to write this testimony so that many who are Battling with different kinds of Challenges Can also get cured.

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