If you need a programmatic way to do it, you can use the Microsoft.DiaSymReaderPackage (version 1.0.7.0), and you need to declare a couple other unmanaged interfaces as well. The checkum is computed easily from the files bytes using one of two algorithms: SHA1 or MD5.

Here is a sample console application that displays information on its own source:

  class Program
  {
      static void Main(string[] args)
      {
          ValidateChecksums(Path.GetFullPath("ConsoleApplication1.exe"));
      }

      // this needs a reference to Microsoft.DiaSymReader
      // or redefine its interfaces manually from here https://github.com/dotnet/roslyn/tree/master/src/Dependencies/Microsoft.DiaSymReader
      public static void ValidateChecksums(string filePath)
      {
          if (filePath == null)
              throw new ArgumentNullException(nameof(filePath));

          var dispenser = (IMetaDataDispenser)new CorMetaDataDispenser();
          var import = dispenser.OpenScope(filePath, 0, typeof(IMetaDataImport).GUID);

          var binder = (ISymUnmanagedBinder)new CorSymBinder_SxS();
          ISymUnmanagedReader reader;
          binder.GetReaderForFile(import, filePath, null, out reader);

          int count;
          reader.GetDocuments(0, out count, null);
          if (count > 0)
          {
              var docs = new ISymUnmanagedDocument[count];
              reader.GetDocuments(count, out count, docs);
              foreach (var d in docs)
              {
                  var doc = new SymDocument(d);
                  Console.WriteLine(doc.Url);

                  if (doc.Checksum.SequenceEqual(doc.ComputeChecksum()))
                  {
                      Console.WriteLine(" checksum is valid.");
                  }
                  else
                  {
                      Console.WriteLine(" checksum is not valid.");
                  }
              }
          }
      }
  }

And a sample helper class, native interfaces and coclasses.

  public class SymDocument
  {
      // guids are from corsym.h
      public static readonly Guid CorSym_SourceHash_MD5 = new Guid(0x406ea660, 0x64cf, 0x4c82, 0xb6, 0xf0, 0x42, 0xd4, 0x81, 0x72, 0xa7, 0x99);
      public static readonly Guid CorSym_SourceHash_SHA1 = new Guid(0xff1816ec, 0xaa5e, 0x4d10, 0x87, 0xf7, 0x6f, 0x49, 0x63, 0x83, 0x34, 0x60);

      public SymDocument(ISymUnmanagedDocument doc)
      {
          if (doc == null)
              throw new ArgumentNullException(nameof(doc));

          int len;
          doc.GetUrl(0, out len, null);
          if (len > 0)
          {
              var urlChars = new char[len];
              doc.GetUrl(len, out len, urlChars);
              Url = new string(urlChars, 0, len - 1);
          }

          doc.GetChecksum(0, out len, null);
          if (len > 0)
          {
              Checksum = new byte[len];
              doc.GetChecksum(len, out len, Checksum);
          }

          Guid id = Guid.Empty;
          doc.GetChecksumAlgorithmId(ref id);
          ChecksumAlgorithmId = id;
      }

      public string Url { get; private set; }
      public byte[] Checksum { get; private set; }
      public Guid ChecksumAlgorithmId { get; private set; }

      public byte[] ComputeChecksum()
      {
          HashAlgorithm algo;
          if (ChecksumAlgorithmId == CorSym_SourceHash_MD5)
          {
              algo = MD5.Create();
          }
          else if (ChecksumAlgorithmId == CorSym_SourceHash_SHA1)
          {
              algo = SHA1.Create();
          }
          else
              throw new NotSupportedException();

          try
          {
              return algo.ComputeHash(File.ReadAllBytes(Url));
          }
          finally
          {
              algo.Dispose();
          }
      }
  }

  [ComImport, Guid("0A29FF9E-7F9C-4437-8B11-F424491E3931")]
  internal class CorSymBinder_SxS // from corsym.h
  {
  }

  [ComImport, Guid("E5CB7A31-7512-11d2-89CE-0080C792E5D8")]
  internal class CorMetaDataDispenser // from cor.h
  {
  }

  [Guid("7DAC8207-D3AE-4c75-9B67-92801A497D44"), InterfaceType(ComInterfaceType.InterfaceIsIUnknown)]
  internal interface IMetaDataImport // from cor.h
  {
      // we don't need to use what's inside
  }

  [Guid("809c652e-7396-11d2-9771-00a0c9b4d50c"), InterfaceType(ComInterfaceType.InterfaceIsIUnknown)]
  internal interface IMetaDataDispenser // from cor.h
  {
      void _VtblGap0_1(); // skip 1 method
      IMetaDataImport OpenScope([MarshalAs(UnmanagedType.LPWStr)] string szScope, int dwOpenFlags, [MarshalAs(UnmanagedType.LPStruct)] Guid riid);
  }